ES, did you ever figure out your overheating issues fully? I'm considering this swap since I have the motor just taking up space in the garage, all looked pretty straight forward to me.
Sorry for the hiatus, but it's been insane this year. Bought a house, expanded the office, evacuated from said house for forest fire, caught in flood on I-70, and now dealing with flood damage on a house I've only had for five months. <img src="/forums/images/graemlins/frown.gif" alt="" />
Anyway, I'm still plunking along with the swap. I've learned some stuff and fixed some stuff and am STILL fixing some stuff ...
The overheating problem - yea, that's still a problem. The new radiator helped. Fixing two HUGE vacuum leaks helped. A few other minor things "helped". The problem remains - the 3.0L engine ECU has too much timing for the 3.5L engine. As I think I posted before - it's like tuning a 350cid Chevy SB vs a 350cid Pontiac. Sigh. The timing issue if not resolved will get worse the lower in altitude you get and the hotter ambient air temps are.
Another thing that came up this spring was the gearing. With the 3.0L I was running 5.38s. That gearing worked "ok" with the 3.5L, I guess. It was nice on the highway in the mountains at 7-8K+ feet, but the lower in altitude you went, the more annoying the gearing was. In a somewhat successful attempt to "force" the ECU to pull timing and reduce the overheating I dropped gears to 4.90s. That worked kinda - nothing great but it helped a tad.
It helped A LOT with the 'annoying gearing' part, though. The problem with the 5.38s is that from a stop I blow through the torque curve before you had a chance to get the vehicle barely moving. At 4K feet in Moab it was even worse. It was like driving a tractor or having a granny-gear first gear. PITA. Didn't do anything for my gas millage, either.
I would strongly suggest to anyone doing this swap at sea level going with 4.63s if you're streeting it and NO DEEPER than 4.90s for mixed use. There's enough torque in the 3.5L that with big tires and a little injudicious use of the gas pedal its possible to pop something in the drive train. In my case probably a u-joint. Keep in mind that messing with the overall ratio can do unpleasant things to the ECU which will affect the ability to pass emissions, so ....
I put the ECU/ECM swap on hold. Its mostly wired but I had to stop work on that to deal with a bunch of other things - including a minor redesign to my cross-over steering to fix a long standing problem that left me stranded. Amazingly enough, in May it DID actually pass emissions. Barely. I'm not entirely sure they didn't do some hokey magic to accomplish this. They tested it twice and fiddled with stuff on their equipment that looked somewhat suspicious. Given the way the thing smells I find it hard to believe it validly passed. But, who knows ....
I decided to go the AEM F/IC route as the 'simplest' and quickest possible fix. I ordered that and its showed up last week. Now I have an Innovate LC-1, the AEM F/IC 8 and the Boomslang patch harness so I should be good-to-go.
I used ScanXL and built a bunch of graphs to map timing, MAP, STFT and LTFT, temps, etc. to be able to figure out how much timing and fuel has to come out and where for the F/IC. I have the maps for my big Sport with the swap, but I still need to get the baseline mapped from my stock '97. Its currently on loan to my friend while I'm having her '98 rebuilt.

Can't start tuning at least until I get the base maps. Sigh.
The mechanical swap itself is pretty straight forward. Just make sure you have all the little pieces, 'cause some aren't available from the dealership anymore and yards typically won't sell them individually.
AND, be prepared $$$-wise for the cost of doing the electronics piece.
Edward