Well, I'm starting to fuzz out, so bear with me. I'm assuming that the one gear grinds and it just won't go into gear like before.
If so, then it means that the clutch is not releasing again. The question is why. There are several possible causes, and you are going to be stuck with figuring them out. All we can do from here is give advice.
First of all, the fork inside the bell housing that moves the throwout bearing can only travel so far. If you were to adjust the clutch linkage too tight, it would bottom out before your foot hits the floorboard, and then something would have to give.
That might be what caused your bending problem.
You need to get under again while the wife works the clutch. Remember to chock the wheels.
Watch the linkage coming out of the bell housing. I think you can see it on that model.
If it is not moving as much as it seems like it should, you need to see why. You mentioned changing holes, try it back in the original.
Just off the top of my head, it sounds like you may have bent something else you did not notice and the clutch is not moving as far as it should when you press the pedal.
You can carefully try starting it in gear. If it was the pilot bearing, then it might break loose for a little while.
If the truck had been through deep water, and then sat for a while, then I would think that the clutch disk may have rusted to the flywheel.
Or frozen to it. I had that happen one morning after a sudden freeze when I had crossed a river the day before.
All I can suggest right now, is watch the clutch arm and see if its moving right, and if not figure out why.
Also, you might try shaking the arm that comes out of the bell housing with the clutch released to see if it might have come loose inside.
You may wind up putting in a new clutch and/or pilot bearing, but lets make darn sure its still not the clutch linkage first.