if you can, i'd upgrade them now, i think the 4cyl stuff is smaller than the v8 stuff, and i dont know if i'd even trust that. i did a 93 cobra booster and cylinder to be on the safe side with my cobra/drum setup, plus its already done if/when the switch to rear disk comes.
keeping the rear drums, you wont need to touch the valve. if you do upgrade cylinders though, you'll need a 3-2 port conversion.
Here's some help - this site is tops for brake upgrade info...
See 87-93 Mustang 5.0 Brake upgrade pages. Improve your 60-0 times! for the best and cheapest brake upgrades and 5 lug swaps. The site doesn't sell anything but some fittings, but the tech notes are great. It tells you what junkyard or remanufactured parts to use to upgrade your brakes. It has almost everything you could want to know about Mustang brakes on it.
If you do NOT change to rear disks, you might now need to change the master cylinder. It depends on what caliPers you run up front? Reason being the cobra calipers have similar piston surface area to the stock 60mm calipers. Therefore if you swap calipers with similar area, the pedal feel stays they same.
I don't have my handy chart with me to tell you how clOse it will be.
And yes, you should gut the stock prop valve and install an adjustable valve.
Run a 93 Cobra booster and Master cylinder, Then get the ford racing plug for the stock prop valve and run an adjustable prop valve for the rear brakes.