That engine looks very clean. Did he tell you why the exhaust manifolds were either repainted or replaced?
I moved my crossover tube not because it was overheating but because my temp gauge was moving around alot and I thought it might be collecting air in the heads. Once I moved the tube I feel like it was more consistent, but that might be me just wanting to believe it made a big difference. Either way I sleep better. I would say run it and if it seems to behave like it should than don't stress it.
I like that high mounted alternator. Is that stock or an aftermarket setup? My 98 is low mounted, so the belt comes straight across from the crank.
Post more pics. Can you show us the details on were the two small braided hoses coming from the exhaust elbows lead?