The problem with your 46 if stock is that the master cylinder will interfere with the shift levers of the saginaw. Also you'll need another bellhousing (or an adaptor plate) as the 46 housing has a different trans pattern than the later transmissions.
I've been down this road that you are taking, can be done but plenty of headaches. I finally opted for the T-5 trans (no side levers) and an adaptor plate, trans to old bellhousing. You can use a 1950 or so truck bellhousing for the late trans pattern, but then you'll have to modify it accomodate the master cyl bracket etc.
Best advise I can give you is to contact Buffalo Ent. ph. 360 652-7684, this man has all the solutions to adapt later trans to your old truck.
