I helped a friend of mine bring home a MK3 Escort convertible yesterday. Already gathering information as he's already got a S1 engine lying around.

MK5 and later Escorts had the same bellhousing like your Escort MK3 with the four stud mounting pattern. So you can use (as a spare) ANY MK5 Escort and later BC box. Important: You NEED a front starter one.And keep in mind: RS2000 16V and some 1,8 Zetec (especially the 130 bhp version) and turbo diesel cars had a MTX box which is totally different.
Easiest to find would be the last 1.4 CVH EFI (PTE) boxes. Mostly the same gear ratios as your S1 plus from 96 on it's a IB5 box. Means you can use the Puma/Fiesta '99 Zetec-S linkage. These came with a shorter throw.