Hmm... Well, at the risk of giving away how redneck I can be at times...
The passenger side manifold on that engine wouldn't come loose. Broke a stud off even with the block, and started to twist a second off, so the passenger side on that E99 block stayed there. I originally planned to swap both manifolds, as my 02's were in much better condition. I eventually had every stud drilled out and heli-coiled on the passenger side. Do yourself a favor and never install and engine with something questionable, just because you need the truck...
The drivers side manifold on the E99 I had was definately different. I don't remember which anymore, but either the E99 mani or the 02 mani has a slightly different turn up, and requires a longer up-pipe.
The rotating assembly needs to be balanced brother.
Wish is was that easy though.