L67 to L67 swap (electrical and vacuum questions)

I'm just about done swapping the engine out of my 97 GTP. I'm replacing it with another L67 from a 2002 GTP. I've had to replace the alternator because of the different designs, but other than that, are there any other pieces that need to be swapped? The engine that I got was only the long block so I'm using some of original bolt-ons including the 97 PCM and wiring harness. The wiring harness looks like it hooks up just fine. My questions are:

• Are there any differences that I'm going to need to be aware of between the wiring harnesses if I'm using the 97 harness?
• The BBV connects via vacuum line to something on top of the SC that has two additional nipples. Are the hoses plugged into it interchangeable and what are the other two items that plug into it? I think one is the vacuum brake booster but am stumped on the other one.
• Where is the "To Accessory" vacuum line connection?
• When connecting the battery, what could cause wires to smoke when connecting the negative cable to the battery?

Thanks for the help!!

as for the smoking wire situation.. follow the wireing and see if something is grounding out.. thats whats going on ... just finding where is the kicker

Back when I removed the starter & solenoid I ziptied the two wires attached to it but there is what I believe (according to the alldata diagrams) the positive battery cable which I missed in the zip-tying if it's supposed to go on that same post. I put it on that post. I think I might be missing a ground on the transaxle side just opposite the starter assembly though.

Also, the smoking is coming from the wiring harness that extends from the ICM in front of the engine to the main wiring harness. That plug (C110) is where the smoking starts and continues to the junction of the wiring harness.

The vac tree with two nipples-one is for the BBV the other for the FPR
The other tree closest to the TB IIRC is for the Brake booster, Map, and the vac line coming up from the fender well on the passenger side.

Vauum is vacuum as long as everything is plugged to a source it won't matter. Personally I prefer the FPR to have its own source instead of teed off something else.

Move over your evap switch and purge valve. Those are specific to your year. You can use the 98+ vacuum setup. It's simpler. Basically it just makes a horseshoe around the engine.

Check your starter wiring. The main cable has a red collar on it, the other two are orange and black. The negative side goes to the trans bolt/stud and has the negative cable and two black wires going to it. That harness you say is smoking ...... well it shouldn't be. Take a closer look at the harness where it goes down behind the ICM bracket and head. Did soemthing get pinched?

I'll be going back up to where she's garaged in a few hours so I'll start with everything there and let you know what I find.

Well after getting the wires situated properly on the starter the beast live(s/d)! After running for a few seconds with no codes I start to get a knock and smoke coming from the area of the spark plug wire number 4 (back of engine, middle plug) and my scan tool reads P0304, Cylinder 4 Misfire and that's it. I checked the compression of that spark plug and compared it to one of the plugs on the front and there was a huge discrepancy (40 on #4 and 105 on the other one I tested (#3 I believe, front of engine middle). While I was under the vehicle earlier connecting everything up the rear knock sensor seemed really loose. Could a bad rear knock sensor be causing my issue? These are new Bosch iridium plugs and new (Duralast I think) spark plug wires. The engine itself is a warrantied and tested engine that had proper compression. Any ideas of what it may be or anything else I can do to try and narrow down the issue with? Thanks a bunch for all the help already given! The car has at leasted started!! XD

Oh I forgot to mention, EVAP purge and switch weren't included with the new engine so I kept those attached. Could a vacuum issue also cause the knock in a single cylinder?

EDIT: I swapped injectors 3 and 4 over, thinking it may have been an injector problem, but the knock didn't travel with the injector and injector 4 still shows a knock and I'm still getting smoke from the middle rear of the engine... :-\