Both the manuals you linked to should work well - I like the Honda shop manuals myself, but others can have additional helpful info, especially British ones. I rebuilt an MR175 motor top to bottom over the winter using an MT125 gearset, and ended up using sections of four manuals.
If your budget allows - I spent nearly $200 just on tools - you should be able to do it, yes. If you're looking to do a complete bearing / seal replacement, many of the parts needed are discontinued and may be hard to find, as I'm sure you're aware.
That eBay crank looks like it may have damage to the threads, taper, and possibly keyway as well. I had my crank balanced at Crank Works, but mainly because I was using a CR125 ignition rather than the stock flywheel ignition. I don't know about the availability of MT125 or CR125 rods / bearings / crankpins etc., but it's got to be better than MR175 parts.

If you haven't already, I'd pull off the entire clutch and then recheck the crank and gearbox rotations.
Ray