Scott..I think it's the 01 in question. I know..99 is also mentioned
The trans cooler lines shouldn't be an issue.
The only potential issue I see si that the 00 might be external park/neutral switch and the 01 might be internal. If so..this isn't a huge problem. It's pretty easily solved, but it's one potential thing.
As for the final drive ratio. I'm pretty sure that the Intrigue being a W body like the Regal .. would also get the 3.05. You can also use Bonneville as a donor.
If you look at your transmissiion where the cable is hooked to the arm to tell it which gear to move into..is there a black item under that arm or is there nothing around the shaft? That's the PNP switch I was speaking about.