It really is the same except for the tail case. The gear ratios changed ever so slightly. Bill Verburg (go figure) recently shared some gearing details.
http://forums.pelicanparts.com/porsche-911-technical-forum/571179-g50-transmission-gearing-question.html
Later on I believe Porsche refined the mainshaft for 993s to take some weight out of the trans. 964 and 87-89 are virtually identical from the intermediate case forward. Only the tail was changed to work with the revised rear suspension of the 964 with coils.
Good idea sticking with the '79 SC. Good car....
Should be able to make the 964 fit.
Some have had to cut into the torsion tube even with the regular G50. Do a search for user JohnJL or something like that. Terms like G50 short bellhousing should get you some more detail than my aging 38 yr. old memory stressed out by work, kids (#2 on the way), racecar tuning (lack thereof), home improvements (lack thereof), blah blah blah.
Don't sweat cutting the tube since even Chris had to clear his a bit and grind on the trans case (early G50). Coilovers shouldn't be a big deal for you! Just gusset the top member and enjoy the better setup of coils!