Computer won't have any problems, if people can swap a 3.2 out for a 3.5 using the stock 3.2 computer, the 3.5 shouldn't have any issues, it's been done before. If you want to not do ANYTHING to swap then you need an engine from a VX but swapping intake manifolds is not a hard task, it's cake work compared to swapping the engine out. You wouldn't have to rig or modify anything, just swap the intakes, should all just bolt right on. Now the later 01' and up engines went to an ION Sensing system but the engine will still swap over using your stock electronics, it still has the crankshaft sensor etc that your current computer would need.
And lfranz, that long block route sounds like a good deal!