Tranny swap

I currently own a 94 jeep wrangler. I am fixin to go to a Lumina, but a current problem on my Jeep i am trying to figure out. I swapped the tranny with a 91 tranny when the original stuck and wouldn't shift. One problem is that the bolt holes for the bellhousing to bolt to engine were rusted and broke in half taking it out. i did some f=grinding on that little angled metal on the block to create a flat surface and put a bolt with washer in place and it holds good with the bellhousing flush against block. I also had to create a new pilot bearing setup due to the end of the 91's shaft being smaller diameter. did this no problem. new clutch put in right before tranny swap. However i am getting a slight squealing noise when clutch engages but no slippage or feeling of bad clutch. i am curious as to whether or not this is an issue that needs addressed and what may be a possible solution

I'd check the driveline angles to make sure everything is straight, and lined up properly.