Man, where to start . . . .
FIRST, have you really decided to truly sink these $ in an old Rick? I'll consider you have, so here goes . . .
Strip all the mehanicals and electronics, and strip the finish. While it's 'raw', have the finger board pulled, install the repalcement truss rods, and reseat the fingerboard. Have it refretted while the board is off, and BE CAREFUL if this 4001 has the triangle/glitter fingerboard markers.
The 'big' Rick pickguard will hopefully cover a lot of the routs you won't need anymore, depending on what electronics you go back with. Anything that needs filling should be filled and sanded while it's stripped. Make a final decision on your components and build out from there. I'd use ALEMBIC Ric Activators to maintain a Rick identity, and they'll fit the pickguard. Any battery routs, etc., need to be done BEFORE you refinish.
Go back with the BadAss if you like, but I'd suggest Grovers like Most Ricks use. A set of HipShot Ultralights would work too. I've rarely seen Ricks with Gotohs, plus the holes in your peghead from the old keys are probably too big, anyway.
Refinish, then reassemble, and you're done. If this was a solid finish instrument, don't be surprised if the wood you find after stripping is not real pretty to use for a see-thru finish.
I can't stress enough to use a FIRST rate tech for this if you can't do it yourself.
But it ain't gonna be cheap. For the same money, you could find a used 4001/4003 in much better shape, change the pickups, and you're home.
J o e y