I did switch back to the correct throw out bearing, and after my playing around, if I went to the longer collar (how I simulated going back to the large on that it came with) the fork is wedged hard against the front of the opening. Now the fork is sitting exactly where it should, but I just have the incorrect slave cylinder. I think the fix I have done with the pin will work perfectly.
The moustache bar is something I will look further into, as there appears to be several different ones, but I should be able to grab one.