The two notable things that are different are the plate that fits between the block and bell housing and the engine mount pedestals. As long as you get a complete 3.5L, including accessory brackets, manifold, etc. its pretty easy 'cause, as you've found out, almost everything is the same between the 3.0/3.5L.

OH, and you may need to make your own throttle cable bracket.

Thanks to your site, I knew all that going in

I got extremely lucky. The truck I pulled the engine from was wrecked, so that means it was drivable before it ended up in the yard. It was also half off weekend, so I got the entire long block (minus the alternator and AC compressor) for $150 out the door. Even if it's ruined, it'll still yield a ton of usable parts.
Someone had also yanked the motor out of a 3.0 Sport, and they just left the motor mounts laying on the ground. I just walked by and picked them up. How convenient is that? One of them is the same exact part as what's on my Max, and the other one is very similar. So now I've got good cores to cut up and use with my 3.5 block plates.
The 99 Montero ECU got here Friday. I haven't dumped the ROM yet. It's MD361885. 3 connectors, no integrated TCU, 3.5L engine. I'm expecting it to be like the 3000GT and Eclipse ECUs where the engine code was the same regardless of whether it was an auto or manual. The only communication between the engine and trans computers was a torque reduction signal and a park/neutral signal. If you leave the torque reduction disconnected and permanently ground the park/neutral line, it's enough to convince the computer it's in an MTX car.
I had actually gotten an integrated PCM to start the engine in my 6 speed Stealth, but I never took it any further than that. It was mostly just to see if it was possible in case we had a hard time getting standalone ECMs. The ECMs ended up being a better option all around, and they were a little easier to come by than we originally thought.
The only other thing is the immobilizer. That can just be disabled. It's been a while since I read up on it, but I think the trick there is to just set the immo code to FFFF. Worse case, I can bypass the immobilizer routines completely with some minor code edits. I've done a ton of work on the 3000GT code, so I'm not expecting any surprises in the truck code.
It'll be a little bit before I can get my plate clear enough to tackle this project in earnest, but when I do I'll post a thread about it.