I prefer Duplicor's engine paint primer.
And I use Duplicolors' ford semi-gloss black engine paint everywhere too. If you're careful with this sprayer, you can get a very nice finish with the semi-gloss black:
And for the truckbed liner, I use Rustoleum. I find it is not anywhere near as rough as what you would see in a truckbed, in fact, the surface is not even very orange peely, but it is in some sense "rough" as compared to paint. Good thing is, if you put it down on a good primer or primer or bare metal... it is not coming off, and it is hard a nails!
I've had mine in the wheel wells for about 15Kmi now. I just went and wiped the road dirt off with a damp towel, and this is what it looks like behind the drivers wheel:
Now, for caulk? I am struggling to remember.. I wanted something that dried pretty hard and would accept paint. I didn't want it too silicon-ized because even cured that stuff is very rubbery. I found something at the HW store, but damn if I can recall what it was.... It needs to be something a little more flexible that JB weld, but significantly less than silicone (if JB weld is a 1, and 100% silicone is 10, you want to get something in the 3 to 4 range. This is so the paint or bed liner wont chip off the caulked surface easily. And you don't want it too hard because as the body panels move relative to one another (pot holes on teh road or whatever, it needs to give some). and when you put it in and it's cured, I cover with primer paint or truckbed liner immediately, so it has a fresh surface to bond to.
Hope that helps.
Jay