I'm pretty sure a baffled sump isn't necessary on a K series car. I don't have one and have tracked mine a bit. I'd ask Lithopsian though!
If it helps, when I put a replacement second hand engine in my car I had Gav put a new mls head gasket on - no head skim and no new type oil rail. 20k miles later it's absolutely fine.
He also put a new water pump, cam belt and tensioner and head bolts on. Plus oil, filter and plugs of course.
Oh, and a new clutch. They aren't that dear so seemed daft not to. I kinda wished I'd put a lightened flywheel on too for quicker blips when heeling and toeing but they are expensive...
I left the 'new' alternator on the engine and kept my old one as a spare which I haven't needed yet.
I wonder about your old gearbox. They are very robust so I'd be surprised if it's knackered. I have Redline MT70 oil in.mine and the change is good. Could it be linkages and cables that are knackered/needed adjusting?
I would keep the ratios from the box that came standard in your 120 bhp car as the ratios are nice and close. It does about 20 mph per 1000 revs in top so it's quite busy but if you're not doing much touring it's fine. It's what I have.