I know the version 4 is a phase 1 and version 5 is a phase 2, but other than that, are the drive trains very different? I just wonder if it would be regrettable to put a version 4 drivetrain into a 99RS instead of a version 5 or 6.

lets see
differnt injectors
different intercooler options
and you can't use ecutek on a ej20k.. ecutek does do ver 5 with flash 99 now finding a ecutek dealer in the us that has flash 99 is another question

As far as I know, the transmission case designs are different as well.

As a data point, RalliSpec sells two different versions of STi and STi/RA gearsets... one set is v4, the other set is v7. The v4 gears are specific to pre-MY98 US cases, and v7 for those manufactured thereafter.

They changed a few dimensions, as well as some bearing styles, as far as I know.

/Andrew

edit: however, on the large scale (entire transmissions, motors, etc.), I believe that the parts are pretty compatible between the two versions.

As far as I know, the transmission case designs are different as well.

As a data point, RalliSpec sells two different versions of STi and STi/RA gearsets... one set is v4, the other set is v7. The v4 gears are specific to pre-MY98 US cases, and v7 for those manufactured thereafter.

They changed a few dimensions, as well as some bearing styles, as far as I know.

/Andrew

edit: however, on the large scale (entire transmissions, motors, etc.), I believe that the parts are pretty compatible between the two versions.

Ver. 7's are 6 speeds. I assume you know this and meant Ver. 5+.