Kip besides what Don has mentioned and what you have already considered there are a few other things to keep an eye on. The 250 is about 2 inches or so longer than the 216. Moving the engine as far back as practical helps and moving the radiator as far forward as it can go also helps. After that the next situation is the fan will be lower on the radiator with the 250 than with the old 216. This isn't the most effective place for it and it works better when pulling through the upper area. I solved this on my 37 by using a 14 inch electric fan from Parr Automotive and mounting it up just under the tank. They had the thinnest 14 inch fan around and it cools very well.
The other area of concern is you will be using firewall mounted pedals. That is fine but keep in mind those firewalls were never intended to take the stress of pedals being pushed against them. Double up the firewall with a piece of .093 to 1/8 inch thick plate on the inner side to add strength. A few inches all around beyond what it takes to mount the pedal assy is enough. You can either weld it in place or use the pedal brackets mountin bolts to hold it, welding a few 1/2 inch long tacks around the outer edge is better.
A hydraulic clutch and brake pedal combination kit works very well and we did a 36 Chevy this way. Ended up using the bellhousing and slave cylinder assy from a Camaro / Corvette / S10. Any will work as long as it was for the V thingys either the Small block V8 or a 4.3 V6 as the backs of the blocks are the same as the 230 - 250 - 292 family inlines.
As far as a rear end we used 57 Chevy rears in the 36 and 37 hung from Chassis Engineering rear suspension kits. The kit is a bolt in but we had to clean off the 57 spring pads from the axles and mount new ones in the correct location. The center bolt holes have to be drilled further forward on the new pads or the axle won't be centered in the wheel openings of the fenders. This is common and easy to deal with. Just make sure you have the weight of the car on the new springs when measuring how far off center you have to drill.
Good luck. I know you'll find it is worth the effort to do.
Mike