Use the latest GM p/n for lower intake gaskets: 89017825. They should be metal shim gaskets with impregnated sealing material. Don't forget to order the two little yellow o-rings that seal the lower intake to the bottom of the SC. You also should replace the gasket on that little coolant bypass cover that bolts onto the lower intake under the throttle body while you have the intake off -- these do tend to leak over time. You do NOT need to put RTV on them other than in the areas where the heads meet the block (where the intake gasket meets the valley end seals).
Clean the old gasket, sealer, and deposits from the cylinder heads using a razor blade, gasket scraper, and chemical cleaners only. Lay some lint-free towels in the lifter valley to capture any debris you scrape off. Don't be afraid to get out the shop vac and vacuum out the lifter valley after you are done cleaning (just make sure you don't suck up any chemical cleaners as most are flammable and the vacuum motor can ignite the fumes).
DO NOT use a die-grinder mounted surfacing pad to clean the cylinder head gasket surfaces as this can throw finite metal particles into the lifter valley which can get into the oil and trash the bearings. Use gasket scrapers / razor blades ONLY. If there is significant pitting on the surfaces of your cylinder heads where the gasket seals around the coolant passages, you may need to remove the heads to have these resurfaced to correct the condition and give you a good seal.
Follow factory assembly, tightening sequence, and torque specifications during reinstallation of the intake manifold, throttle body, and supercharger.
-ryan
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6+ years on this same swap -- NO engine or transmission failures...
Custom GM OBD1 & OBD2 Tuning | Engine Conversions & more | www.gmtuners.com[This message has been edited by Darth Fiero (edited 02-19-2010).]