Yes engine mounts bolt straight on, but on passenger side only 2 out of the 3 bolts will go in.

Sump, my mate has bought the retro ford sump which was a direct and no hassle fit.
Carbs or injection well its up to you really my mate is going using a bike carb kit which was bout £800 for everything, but that is gonna be for track purely.

Or on the otherhand me and my old man fitted all the original ecu and injection from a mondeo with 'non pats'. It isn't hard at all only a few wires to power it all and for clocks.
But if your not confident with wiring it may prove a bit difficult.
It is alot cheaper and will run sweet as a nut like a mOndeo.

It's up to you really mate.

Gearbox you van use any type 9 5speed except for the v6 one as this has a longer input shaft. Also make sure the starter is on the exhaust side of the bellhousing.
With the clutch there's a few ways to do it. Get a 1800 zetec flywheel and redrill to suit a pinto clutch and pressure plate.
Or
Like we have use the full zetec mondeo clutch system( actually bigger diameter than pinto) and modify the clutch fork or the hole it goes through to get full engagement. Use a threaded adjustable clutch cable. It works really well on our cortina

Hope this helps mate