With a manual box it's not to critical. Both the R25 and R28 will handle the output of a 3.0, especially in a light car.
Gear ratios are here:
http://www.omegaowners.com/forum/YaBB.pl?num=1163895469/0#0There appears to be a small difference in ratios between the 4 cylinder engines and V6s, so a little choice there assuming the 4 pot boxes will fit the V6.
Ultimately, the diff ratio will give you more control of the characteristics.
Looking at those ratios you will probably find first gear very short in a light car with V6 power, and quite a large step up to 2nd, so your choice will probably be between fitting a diff with a short ratio and forgetting 1st gear, effectively using it as a 4 speed box, or fitting a much taller ratio diff and having a useable 1st..4th gear with 5th being rather high - suitable only for relaxed motorway cruising.
Best course of action is the plug those ratios into a gearing calculator - something like this:
http://www.ukmotorsport.com/misc/gears.html .. and see how they look.
Kevin