JayEstes

Here's my take - some of that may be reasonable and some of it definitely is not.  For instance, it's definitely not a good recommendation to put in performance suspension & handling for $5K.  That's NOT mandatory.  You can get new stock UCA's for lass than $50 per side (that's a lot cheaper than $350/side).
Don't put in 620lb springs up front unless you want it to ride like a covered wagon.  I think stock springs are 300 lb/in.  Don't lower it, but instead:   The top 3 upgrades for front suspension improvement are:
Redrill your shock towers to do the "Shelby/Arning drop" (if not already done) with new UCA's ($20 template + $100 for both UCA's) Put in a 1in" sway bar.  (best bang for the buck I think and makes the car safer to drive) $140 New KYB Gas Adjust shocks (Maybe $100 for both) After that, you'll need Tie rod bushings ($40ish), stock perches ($40), new spring seats ($10), some Tie-rod work
So that's like $400, and it will drive fine (not like a racecar, but you won't shatter your teeth going over the railroad tracks either)
On the rear, I would not buy new springs unless they can show you they are bent or ruined.  Just New KYB gas adjust shocks and see how it is ($100), maybe new leaf spring bushings if she's rattly.  Since there are traction bars, this will be more work.
So that's maybe $200 on the rear, and most all the big stuck on suspension for like $600-$700 in parts.  If you do this work yourself (only thing really dangerous in compressing front springs).  If you want to pay to have this done, $1500 is probably not outrageous, but I wouldn't buy new leafs. if they say they are "shot" make them show you how. 
Brakes are most important:
replace all the rubber brake lines, 3x maybe ~$50 each.  The following statement however - makes NO SENSE to me: "Found rear brakes contaminated with rear axle gear oil."  I have no idea how this could happen.  Sound like BS to me, and I would ask about it.  These systems are not connected, and I can't see how they could be thru parts failure, so I call BS.  Get a new drivers drum if you can't find someone to machine it.  New pads (cheap) and get new rear cylinders (cheap).  My brake backing plates are grooved some, but still work ok - weld and remachine is a fair bit of expensive work, and I'd try it without doing that.
They don't mention the brake distribution block or the proportioning valve.  The prop valve should be taken off and have a new seal kit put it - virtual certainty it needs that ($35 for parts).
---
Engine:  That's an expensive radiator.  I bought a 3-row copper for about $350.  You can get a thermostat for $5,  you probably don't need a fuel pipe - I wouldn't do that.  If you flush out the fuel tank, there is no need to move the fuel filter ahead of the fuel pump (non stock).  New rubber connections ($10), New fuel pump $30, new filter $5.  That's all that's required.
If they can show you the leaks on the manifold you should fix it.  And you can look for this yourself, by simply wiping off the front and back and driving it around.  If it's leaking oil you should be able to see it.  personally, I don't need to remove the Ac compressor to work on the intake so - my opinion - not required.
Your oil pan probably is leaking.  Do you need to spend $1000 to fix it?  NO.  This is a hard job to get the old one off and put on a new one that doesn't leak, but honestly, you can keep the oil filled while you save some $'s to have it fixed later for cheaper than that.
Fix the motor mounts.  If they are original, they probably are cracked.  $320 seems like an ok price to do that.  Engine balancer MAY be needed.- if you can't get it to run.  But if it runs/timing is OK, I'd do this later.
For the love of God, do the all the AC/PS/alternator/fan belts yourself - any person driving a 69 oughta be able to do the belts.
No idea on the improvised trans inspection plate, but it's probably fine (it's a piece of sheet metal to keep crap out of the flex-plate starter engage area).  look at it yourself and see how bad it is.
Trans mount is good chance it is bad.  $125 seems reasonable
I'd note the rear axle seals as something to watch, and do them later.  That alone is like $300.
buy your own heater hoses. $340 is outrageous unless he is putting Stainless braid on them.
Elec:
I don't know what he means "seat plugs" but they are dang expensive.  Fix the electrical that's broken and nothing else.  he's only giving you an AC diagnosis, which means there is another $1500 of cost to get the AC going probably.  Can wait.  Two windows at 60mph is usually okay for a lot of the US.
Body:
If the roof drip rails are leaking, that can allow body rust which you don't want.  you are looking at a lot of cost that may affect the paint.  so this is expensive.  Depending on the quality level of your paint, this may or may not be worth it.  Just do whatever to avoid rust.
OMG - do NOT spend $600 on the damn clock - buy a wrist watch!  $35!!!  worst case - pull it yourself and mail it off to be fixed.
Dash: LED light kit and printed circuit panel is all you need.  your fuel gauge either works or doesn't.  If it doesn't, I would change the sender in the tank for $30, and not buy a new gauge (which is probably fine, but inaccurate - they all are BTW).
Steering wheel can probably wait at $1250!!! Good lord!. 
Fix the windows.  those mechanisms probably need an overhaul - they are cheap systems, and if not adjusted properly, can bind and be really frustrating.
UGH.  That's a lot of stuff.  I'm not a fan of having other dudes do my car work, and so I don't know about labor costs.  Anything over $100hr is questionable.  $80 may be reasonable.  My costs above are for parts, not labor (all of mine is free, so I on'y see parts costs).
This stuff is not that hard to fix yourself.  It just takes time.  If you have more $ than time - this shop may not be that bad, but there is some questionable stuff  in here - other stuff looks reasonable.  it's a mixed bag.  
Good luck.
 

Well are those prices parts and labor?
$340.00 for heater hoses?
I would post exactly what radiator they are suggesting because it is likely pos small tube chinese one. I have a real 3 row large tube original style rad here that has a new us made core for sale.

What to fix first?
Make sure your checkbook and/or savings account is 3x larger than what you think it needs to be.

I just had barely related thought about exhaust back pressure. I've heard from some who should know better that engines run better or make more power if the exhaust system has some back pressure. Anyone ever heard that? I think I heard it in a muffler shop once as well as in a speed shop. Is there an emoticon for rolling eyes? It can often be difficult explaining the truth. I'm sure that isn't the case on this forum :-)

From the gasket imprint on your cylinder heads, it looks like the gasket wasn't covering the tops of the intake ports.  Hence, the large vacuum leaks.  And from the gasket imprint on the intake manifold, you had the wrong intake gaskets for the rectangular shaped water ports on the cylinder heads.  Try the Fel Pro Performance or the Edelbrock intake gaskets I referred to on your other thread. 

Fixed my passenger side sport mirror.  Watched a video from West Coast Classic Cougar and tightened it up so it stays put when I drive before I put new mirror glass on it.
Installed new medallions on the sides.
Just ordered an original 69 C9Z AM Philco radio,  It did not have knobs but I think I have some.  Yelling at 16 year old me for losing that original radio.

I might honestly be salivating looking at these engine pics.... 

Installed a new harmonic balancer, clutch disc, pressure plate, & the bell housing.
 

Today I removed the engine from its stand & put it on a dolly & installed the flywheel.
 

Installed the water pump, intake manifold, distributor, & dip stick.
 

My guess would be air in the lines. Did you bleed them when the pump was replaced? What are you using for power steering fluid, type F trans fluid I hope...

Heads are assembled complete. I had 2 valve seats that didn’t pass blue check. I lapped those two in (was very minor) and all is right. Springs went on easy. Jim is happy.

Blasted, primed and painted my rocker trim.
Yesterday did interior pieces.

fantastic news!

I used what used to be GPS, now LEEDS.  They are out of Niagra NY.   I bought the booster, master cylinder and pedal assembly.  All pretty reasonable.  So far so good.  I had to cut part of the dash away to make it fit and they provide the pattern.  I think that works with any of these.   I still have my FMX in the car.  Not sure if that will make a difference.  
https://leedbrakes.com/
 
 

You nailed it. So grateful I thought I was up for another rebuild. I took the old fuel pump off and blanked the hole. Quiet as a mouse. Thanks.

Bolted on a wilwood master cylinder, powder coated the dash vents and now I'm replacing the felt lining 

No pictures, CV?  Shame on you!
Respectfully, the Evil One.

Looks great. I went with Evaporust as it got good reviews and was available close to home. It’s applied, bagged, and we will see tomorrow how it did.
Also got my cam bearing tool today and I knocked out the old cam bearings. I have everything I need to finish the short block now.  Waiting on springs and valves to do the heads.

Regarding painting the engine:  I think you definitely want to kill that rust on the engine block.  I use this spray on acid “osphor” that I get at my local hardware store.  Just spray in on the surface and let it sit for several hours or overnight.  Then I use a wire brush wheel to clean all of it off I can, then hand wire brush tight spaces, then I clean the surface with laquer thinner right before I put the paint on.  
I recently repainted my intake (while installed) like this and it came out nice- paint seems to be sticking well (I only used 500deg duplo rattle can for this- approx 3 coats.)
 

 

Thanks, I got one today.

+1

engine compartment walls could use some cleaning and paint.  Maybe some Ni/Cu brakes lines bent and installed.  And while you've got that stuff out, I'd suggest a full rebuild of the steering and suspension...  I mean, you know, SINCE you're in there.