ford pinto + type9 fits quite easily, points to watch out for are:
you'll have to mod gear lever hole but gear lever will foul handbrake - move handbrake or shorten handbrake ( i did the latter, wasn't great)
some bulkhead re- dressing required but not much
you won't have to enlarge the tunnel either, it all fits in
Ford xflow + standard 4spd ford box all fits in easily :
no bulkhead mods
no tunnel mods apart from gearlever hole which again means the gear lever problem, but if you fit an earlier 3 rail from an anglia or cortina then you wont have to sort the handbrake.
essex v6 + standard v6 box (2.3 = no bulkhead mods, 3.0 = not sure about bulkhead, but there cant be much difference between the deck height )
gearbox fits tunnel, but gear lever hole mod needs doing
steering column fouls oil filter so you'll need a remote housing, still tight though.
these are all mods i have done in the past ... with some overall success , xflow was by far the easiest, and the most fun. And where a xflow goes, a zetec will go
...but not the SE or sigma unit, that is a duratec and will not fit standard ford RWD boxes...although i believe it will fit an MX5 box ...which means you could fit a 6spd box
yay
don't quote me on that though :/
zetecs are cheap and plentiful, and will run happily on carbs and aftermarket ignition boxes. The 2.0 will require some head scratching regarding the pumps and pulleys because they run backwards, and they all need a water rail/thermostat housing mod.
But, in mentioning a MX5, ,you could just buy a scrap one of those and chuck the lot in, good engine, nice box, all in one package....food for thought