Just what do you really want to do with this car? There is no point in doing everything twice. Do you have the proper equipment? MIG or TIG welder? garage space? just how rough is this car? Do you what 5 or 6 lug wheels?
As said, if the current drivetrain is in working order, the '60 engine can be swaped out for the 216 and reuse everything else. The waterpump may need to be shortened and the front motor mount may need some attention, but that should be most of it.
The next option would be all of the above, and to swap out the rearend for one from a 50-54 car with powerglide tranny as these had 3:55 gears. It will have 5 lugs, but your '48 axles and drums can be swaped if you want to stay with 6 lug.
Option #3 : I haven't tried this, but it makes sense to me. Using the 47-54 truck 3spd with the later bellhousing and the 3:55 rearend. The reason I say it should work is that the 50-54 'glide rearends have been swaped into both 41-54 cars and 41-54 trucks. I would measure the distance from the bellhusing to the axle centerline of both just to be sure. Your '48 and the 47-54 trucks both have a 116" wheelbase. The other issue here would be hooking up the column shifter.
Column shifter. Obviously I know nothing about vaccuum shift, or how your H box is setup, but I would think that if it has 2 arms, then it could be modified to work (change length of arms), since the later ones that Hitork mentions have 2 arms. But if it has only 1 arm, then swapping out or going aftermarket to Buffalo's as mentioned could be the solution. the other choice would be to convert to a floor shifter.
Open driveline. You will need the later bellhousing. You can use almost any '55 or newer tranny, including the T5. Truck rearends aren't really suitable as they either have lousy gearing or are too wide/narrow. In other words, your 6 lug options are very limited. The only ones I know of would be the 55-59 1/2 ton, 4X4 blazers (years??), and possibly some import trucks (Toyota, Nissan ???). The 55-59 are a couple of inches wider and do not come with good gearing, which means buying aftermarket 3:36 gears ($$$$) to make it useful. I have heard of guys using the blazer rearends in the 47-54 trucks, but I don't know what years or if it's the big or little blazer they are talking about. Same for the import rearend. Don't know what years, etc...
5 lug car rearends would be the better choice. 55-64 works, '70's Camaro/Nova as well as others. One thing to consider is what you intend to use for rims, as having them stick outside the fenders is not a good idea. Most aftermarket rims can be ordered with a variety of backsets, but you should consider this when choosing a rearend.
Automatics. Don't. It will cost you alot more money, it will be more work to install correctly, your gas milage will drop, and the performance will suffer.
Sources. Try Hemmings Motor News. This is the best overall source for anything automotive. Get a catalog (or go online) for every vendor that you think you might do business with and compare. Gives you a better idea of what it takes to fix something up. You are from Chicago area? there is a salvage yard near Watertown, WI called Jack's Auto Ranch 920-699-2985. They have dozens of 46-62 Chevies rusting away, the parts in question are all there, just not sure about price or condition. Be prepared to spend most of the day looking around. Take a camera and tapemeasure. One of the biggest swapmeets around will be in Jefferson, WI on April 26/27?? Also a small one in Grayslake,IL on Feb 23. Also 2 in Waukesha, WI one in Elkhorn,WI another in Jefferson in the fall, Iola, WI in July. And Goodguys is having an event in Waukesha later this year. Try doing searches in the yellow pages for other salvage yards in your area and search the "events" section at
www.hemmings.com
