Sorry for no update (for anyone who cares) but I’ve actually been working on the car quite a bit in my limited free time. I’m still working some major issues (not supercharger related.)
See the following for the problem/troubleshooting: http://spyderchat.com/forums/showthread.php?45176-Coolant-issues-continue-actually-overheated
85. So I looped the the coolant lines going into the IACV and plugged the two ports in an attempt to fix my coolant issues. Turns out it didn’t make a difference. I’ll probably leave it this way, as I had a previous 2zz with obvious coolant intrusion into the IACV. Might make a slight improvement in IAT, though I doubt it once it’s heat soaked.
86. Since all my attempts to solve the coolant issue had failed, I said screw it and decided to pull the engine last weekend. A bit of a kick to the nuts considering I had just installed a transmission a couple weeks ago. At least now I have the procedure down. I removed all the ancillary parts, to include the header and rear crossmember. I left the struts attached, but pulled the axles from the hubs (leaving them in the trans.) So the engine and trans were dropped still full of fluid. Lowered the powertrain onto a dolly, removed the remaining mounts (left and right) then lifted the car off with the engine hoist. A bit of wiggling and the engine is rolled out.

Now the head is off and on the bench where I’m rebuilding it (new stem seals, cleaning up the valves and ports.) The block and head both checked out with no warping. I’m doing a fine inspection for any cracks, but everything looks fine. It’s difficult to see any head gasket leaks, because the gasket leaves paint residue everywhere. I think the engine is in good order, but I’m at the point of biting the bullet and ordering a new short block. I just want the peace of mind knowing I have a zero hour bottom end, with a fresh top end (already have new cams shimmed to spec.)
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