Dave, with the drive shaft also twisted, I wouldn't reuse the old bearings on it, so I wouldn't be conscerned with them being ruined trying to remove them. There are 2 bearings back to back on it. The bearings are cheap. They are Timken brand. They can be bought from Merc for $20-$30 each, OR just get the number off of them and go to AutoZone. I bought several of mine from there for $5-$8. These are the exact same bearings right down to the packing oil you will buy from Mercury. The ones they didn't carry I bought from a local bearing supplier, again 1/3 of Mercs price for the same bearings. Stay with the Timken brand. Just buy a driveshaft from Merlin and have him install the 2 bearings unless you have access to an arbor press.
But now you are talking about, new bearings, 2 new shafts, more than likely a few different thickness shims to reshim the pinion height and the tools and gauges for setting the drive up. It's not just a case of replacing the bad parts even if you bought a shaft with the bearings installed.
At this point, you might be better off sending your parts to someone who has this stuff and the experience. I never dealt with Merlin540, but with his reputation here on the board, you might check into that route. Course, you tried that before.

The complete used lower your considering is an option too, just bolt on and go. But if you recall, one of my lowers was out of specs from the factory. Might be best to have yours done right and know it. That gets my vote. And it's cheaper.
1 final thought, what kind of shape is your housing in...chipped skeg, cavaitation plate, any corrosion?