"When I check the output side of the turn-signal flasher I am getting approx 3.5volts compared to the output side of the emergency flashers where the power is close to 12volts when energized."
As a test seeing that there isnt enough current to work the t/s flasher make a jumper and put it in its place . Then look for whats working and whats not, bright dim etc. Using a test light to diag these issues (power and ground faults) should make it easier to locate your issue.
As far the side marker light being wired incorrectly (parallel to the front turn signal) it would not cause a t/s disruption unless it was some how shorted and wired to the turn signal wiring and blowing a fuse. Wiring the ground from the side marker to the turn signal wire will operate the light normally when the park lights are on using the ground path thru the turn signal filament to ground. Turn signal operation will take the ground away when the signal light flashes putting 12 volts on the side marker ground causing the light to flash a "wig wag" effect .