CONCLUSION:
To anyone needing to repair a leaking upper and lower manifold gasket, replacing the original plastic lower gasket with a new GM (or other) metal gasket set will solve the problem of the LIM. If, when the LIM is out, you perform 2 minor mods—block off the coolant ports for the TB and enlarge the openings under the coolant by-pass cover (I followed BillBoost37's post http://www.grandprixforums.net/how-mod-lim-46931.html)—the UIM issue may be solved as well. Even with the plastic UIM. It might warp in the future, but there won't be coolant in the manifold. Knowing what I know now, that's what I'd do. The UIM mod is a lot of work (not hard, just a lot).
After dealing with a couple of P0171 error codes, I finally have everything sorted out (I hope). Turns out that hose clamps and super glue are required when making vacuum fittings. Also the EVAP plug on the UIM was leaking air, so I removed the plug and filled the hole with JB Weld Epoxy and put the plug back in. I also had a torn seal on the MAP sensor, so I replaced that. I thought the IAC was iffy, replaced that too. Everything seems to be working as it should now. I am still getting a slight hesitation between shifts under light pedal, and I want to try to find what's causing it, but not now.
I created a spreadsheet of the parts/costs/mods that I experienced. I hope it's helpful for anyone considering doing this mod. Feel free to download at http://bit.ly/14lsgzh . I'm sure there are better prices than what I paid, but this should give you a good starting point.
