Not sure how much work the muffler shop did, but $50 seems pretty reasonable for some pipe, bends and welding.

As far as too simple goes, it is just basic plumbing, nothing that can be really screwed up, except for it fitting, and as long as you plumb it in ahead of the O2 sensor there shouldn't be any issues w/the ecu getting the right info from the O2.

I dug out the old manifolds, if you need them, shipping weight of the drivers side is 10lbs and zip is 95949. I have the oem x-over w/both flanges still on it as well, so if you need them let me know.

Is there going to be enough room w/o a body lift to get the passenger side over to the drivers side down pipe?

More than tread lightly. Leave it like you were never there, nor anyone else.
'90 X-cab 4.88's 33 BFG AT's, rr ARB, Headers, Ignition upgrade, cold air induction.
'91 X-cab 5.29's 315's BFG MT's, rr ARB, custom bumper and flatbed