Well I have a  St. Croix Avid 6'3 M XF spinning with about 6 inches cut off of it so it is about 5'7.

And I have a St. Croix Avid 6'6 MH F spinning with about 3 inches inches cut off of it so it is about 6'3.

Both of these rods are factory rejects. I will probably be using these rods for bass, walleye, trout, and panfish. Do you think these rods will still work well?

Define what "work well" means to you.

Will they serve you ? yes they will

But they won 't work and behave as they were designed for because they are no longer how they are supposed to be, that M XF is no longer M XF if it 's missing 6 inches.

Sure they'll work . How well ? Only you will be able to answer that after you use them.

I don't see either being much use for the lighter applications like panfish and trout. Many fish have been caught on a cane pole or hand line. It really boils down to what your own expectation is of the equipment.

Cut bait for Catfish.