Present and accounted for.
There is no kit that I know of for a Model A on deuce rails. Welcome to hotrodding. A hydraulic assembly will certainly help matters; do your research though as some of the street rod pieces seem to be leak prone.
Some of the guy's who were around in the 60s may remember the Ansen swing pedal assemblies. This is a 'box that has 2 pedals in it (brake and clutch) with their respective reservoirs (I believe). This would certainly simplify things.
With regards to the muncie itself; If you want an M21/M22 you'll need at least a 3.73 rear gear. With the typical tall rear tire on a coupe, you'd really want a 4.11. You can run an M20 with a 3.42/3.55/3.73 or the 4.11 and be happy.
There are aftermarket gearsets that have special ratios for the Muncie. One company makes a version of the M20 ratio on the M22 platform. They're offshore gears. The higher than OEM quality gears are made in italy by 'Masiero' which is now 'Euroricambi'. They're approx twice the price, but if you're running it hard, I highly recommend it. Whatever you get, make sure that the countershaft hole at the front is in good shape; no pinpricks around it, no silicone, no leaks. It'd be better if you could get your hands on the 1" countershaft unit.
Regarding other transmissions: if its just a cruiser, a modified T5 would be great (they're usually 12-1500 from the guys who build them); you could also go with a New Process 833 OD. This was a 4speed overdrive sideshifted GM version of the venerable Mopar 833. It was used in pick up trucks in the late 80s I believe. Its a heavy ****; but it has the benefit of being approximately Muncie sized, has the mild OD and its a 4 speed. A TKO is going to be tough to fit I think.
If you get serious about this, I have a customer who is putting one of our 4 speeds in his 60's style 3w coupe (proprietary 2.98 1st gear with a 3.55 rear gear I think). I can touch base and see how he feels about jumping in here or e-mailing you.