The difficult problem with the tranny swaps (as yes manuals were made available in all non-US markets) is the number of year and model specific variations - cabling and wiring in particular.
All of the 5 speed T5-r and R cars received an uprated 5 speed box which was modified to better deal with the increased performance of these models. The real jewel you want out of one of these cars is the viscous coupling limited slip differential that was used exclusively on the R and T5-r variants.....I'm still scouring the junkyards of the world in search of a donor car for my T5-r!

As for reprogramming your ECU - well you could have the mods performed to make it function properly with the manual, and at the same time adopt a higher performance mapping. Probably more effort than you'd want to put into a garden variety 850 (though you can find a complete GLT with a manual for around 1700-2000 US, swap trannies, then sell your donor back off ^^)
Just a thought......