if the lim gasket is bad or not sealed properly you'll have a coolant leak. the gaskets are crush gaskets and need to be replaced everytime. oil goes into the heads, coolant and air travel through the lim, in seperate parts.

take the alternator to autozone or similar parts store and have them test it, its usually free.

the connectors at the wheels connect to the abs sensor and then connect again to the harness, each side is opposite so you cant screw it up.

i had some small problems when i did the swap and most of it was corrosion on my old wiring harness. i swapped with a 2000 gtp harness and was good to go. i also added the HUD and digital DIC by splicing into the wires, no need to change the BCM.

as far as tuning goes, i joined a local forum and had good luck with local guys helping me out when money is short. lots of good local deals on parts too