You don't mention what you've done with the spider hose, but make sure that you rip it out and block the hole it comes out of - cut an inch or so off the end of the pipe, fill it with JB weld and jam it back into the hole. Put in a longer bolt through the timing cover and put a washer or tab on it to keep the pipe from popping out (it will be obvious once you look at it).
Remove the other heater fitting from the back of the head and make a block off plate; I use 1/8" aluminum shaped with a hacksaw. Delete all of the heater nonsense (unless you think you need it for defrosting, not an issue here in CA).
Do not loop the heater circuit, this will cause coolant to circulate in the head without going to the radiator. Bad. Throw out everything that was attached to the spider hose; you should have only 2 coolant hoses, one going to each end of the radiator.
If you do the M50 manifold swap, ditch the idle control valve and adjust your idle with the throttle stop screw. Plug the hole in the intake boot with the intake air temperature sensor. Plug the IAT hole in the manifold with a screw & some Teflon tape. This is harder to do with the M52 manifold due to the stupid way the oil separator is mounted.
Remove the smog pump, cut off the pipes about 1" from the exhaust manifold and crimp them over to seal (or weld if you're a perfectionist).
Get a copy of RomRaider and the MS41 flash tool from chipster.no. Flash out all the emissions stuff & the rear O2 detection nonsense, cat heating, etc. etc. and ditch all of the related equipment. This will also let you hack out your cats or run a test pipe, etc. etc. without the DME getting all upset at you, and remove a ridiculous amount of clutter from the engine bay.