Almost any GM bolt patterned transmission. (all GM's were the same manual transmission bolt pattern until 1993). Match the front spline to correct clutch plate spline. Match correct front driveshaft yoke spline count to the output shaft spline count. You will need the drilled boss on the driver's side of the block for the Z-bar pivot ball, tab welded to the frame for the other pivot point, the Z-bar, pedal, push rod, fork, fork pivot, or go with a hydraulic release bearing system. May need to shorten/lengthen driveshaft, and possibly move and or modify the cross-member. I have done a few auto to manual conversions. They are complex, but not complicated. (if you have never done one) Just ensure you get all your questions answered before you start, so you know if you want to do it, and what direction, hydraulic, or "OEM/typical aftermarket".
Didn't 65/66 GSs come with Saginaws from the factory. I know my brother's 66 GS had a Saginaw 3 speed and he knocked the rear out on that, never had a problem with the trans. I noticed the Summit catalog it says not for over 250 hp but I don't understand why, the gears and shafts are the same size as a Muncie. I would say the old Borg Warner and the Saginaw are equal.
FWIW, I had a Saginaw 4 speed in my 1964 Special. Came out of a Vega and had great gearing for the engine/rear end. Engine was 330, .060 over. TRW 10.25 and near zero deck. (195 PSI compression test) I lucked out and had W-30 "F" heads and ported them all new valve guides, valves and springs. Cam was .475/328/108 and Q-jet. 3.08 posi. I drove the car for 5 years and really ran it hard, a lot. to and from Florida to Wichita as well as being my daily driver. Never had any trouble with the tranny. Did kill a clutch, flywheel and pressure plate. It was somewhere in the 400 HP range. Pulled to 7k. I never ran it across a dyno, or timed drags, but we surprised a lot of folks, including motorcycles. The best was running a Suzuki GS1000, and the guy caught me at the next light and said he had never been beaten by a car. I just got lucky with the parts coming together as they did. But all that to say that while people may say that a Saginaw is a weak piece, like a lot of things, sometimes people just keep repeating what they heard from someone else. Much like a Q-jet is junk, or Switch Pitch was a problem and that is why GM dropped it, or Buick engines are weak and cannot take a pounding. I think a lot of the problems with the Saginaw's were the same as with anything, if one does not understand and operate the machine correctly, one can expect a rapid disassembly of components. If the OP plans on a full on drag car, then a Saginaw or most any other similar transmission is not for him. But if a weekend cruiser, and occasional asphalt warrior, then any of the three, Saginaw/BW/Muncie transmissions of similar form will be fine. Hope dr is able to realize the "three pedal" in his '62.
These tranny tunnels are really small and not many trannys fit without mods. The BW T-10 was the 4 speed factory option in these cars, but thats the least of the things to deal with in a swap like this. Your pedals (which are rare), linkage, shifter, cross member, drive shaft etc.. are going to be fun and $$$ add up quick. To do the conversion and do it good and right I would plan on a budget of $3,000 by the time your all said and done. But now if your like me (I like top shelf quality @ bottom of the barrel prices) I take my time, do my homework, do my research, then I start shopping around for parts. I have gotten lots of deals on ebay on parts by using "odd search engines", also have got deals on parts off from craigslist, sometimes making a 2-4 hour road trip even. If you get enough good deals on parts you maybe able to do the conversion for $1500 or so. I am doing a similar conversion (63 skylark) from auto to 4 speed. I have a BW T-10 tranny, shifter, clutch pedals and all the linkage that I have gotten really lucky on finding on the cheap, under $800 total. Now I still need clutch stuff, redo the drive shaft, the cross member mount, 4 speed hump etc.. So I'm thinking by the time i'm said and done I'll end up spending upwards of another $1000 or so. And thats doing it the bargain hunter way LOL. Not trying to scare you off, just saying how it is. But having that man pedal sure is great! Keith
I realize its a pipe dream at this point. I have a ton of things to do. I just love the idea. The 350 swap and trans. is going to require a great deal of cutting and fitting.
