1) It is no design flaw, it is the exhaust heat crossover that allows the choke to open by heating the bimetallic spring.
2) A stock exhaust can fit fine even with a rear sway bar, with either side or rear exits. It depends on the skill of the exhaust tech, it sounds like they took the lazy way out.
3) Had trouble getting the AC back on correctly? If it unbolts, it should bolt back up. Unless they lost parts or broke something, or you added late model heads without all the correct holes.
Vikki 1969 Goldenrod Yellow / black 400 convertible numbers matching