R has different bore and stroke depending on years, that wouldn't matter much if you are just swapping the block, you could run all the old accessories like manifolds, turbo parts, etc...and it would all swap over and realistically the ECU wouldn't even mind the difference in displacement and compression, it's a small change and the car would run and drive like normal with the stock ecu. I believe Chilledman can confirm that you can swap in a R block into a 2.4T without any changes in ECU, they cars aren't smart enough to know the displacement. If you were going to run higher than stock boost than a custom tune would be the smart way to go but not needed for the 6psi.
Re: VVT, check that Whiteblock thread on VS i linked to, it has all that info in there plus cam lift, rod size, etc.........
edit here ya go:
2001-2004 2.3 T5 Single VVT
2001-2004 2.4 LPT Single VVT
2005-2009 2.4 T5 Dual VVT
2003-2009 2.5 LPT Dual VVT
2004-2009 2.5 R Dual VVT
funny enough notice that shows a 2003 2.5T LPT Dual VVT, kinda like OP mentioned. I wonder what those came in, did OP ever confirm his engine type?