Yes, they're the same block.
If you can't find an 05+ transmission, you can always buy the 3.82 final drive and replace the 3.41 with it, I have one for sale right now in the buy/sell/trade forums right now.
If you wait a few months I may have a complete 2004 MTX75 from the 2.3L duratec for sale, and I'd be willing to throw in the 3.82 (you'd need to do the work to install it) as I'm currently researching swapping in the Mazdaspeed3 6-speed manual transmission.
cheers,
-- michael