Can motion control shoes be fixed to neutral?

It's too late. You've probably already done permanent damage. Good luck.

It's never to late to fix ANYTHING. Don't listen to the trolls. Work on perfect form and flat mid landing. Do form drills.

Just either

a.) Return them. If you bought them at a reputable running store, then they will probably let you if you've put barely any miles on them

b.) Toss that s**t.

It's generally hard to fix shoes as you have described.

If these shoes are over-correcting your mechanics, then return them, sell them on craigs list, or use them for walking around shoes.

You have perfect biomechanics using what shoes? Why would you ever buy different shoes? Are you sponsored? You just bought a pair of motion control shoes in the store and they felt fine but now you can feel a difference?

Perfect biomechanics. ...what is that?

Use a dremel.

Sorry, you can modify neutral shoes to provide more stability, but you can't turn stability shoes into neutral shoes.

I realize this is not going help the OP in any way, but I just thought I'd relay a funny story from the 80's. I few guys on my team had Asics (Tiger at the time) Excalibur GT's, which had a small, hard medial post. Halfway through the season when that old EVA started breaking down, the post would start digging into the shoe & into the foot. They just got a pair of pliers and ripped that sucker out. Problem solved.

I have more perfect wrote:

You have perfect biomechanics using what shoes? Why would you ever buy different shoes? Are you sponsored? You just bought a pair of motion control shoes in the store and they felt fine but now you can feel a difference?

I loved the old Mizuno Wave Riders, then the 17s sucked. Mizuno publicly apologized so I gave the 18s a chance, but I'm doing more trail running these days and the 18s got torn up quickly and didn't handle rocks well, so I went looking for a trail shoe.

I bought the Brooks GTX because they felt fine in the store (most shoes have too narrow of a toe box for me) when I tried them on without looking up information on them.

I'm going to try sticking some moleskin or something under the insole on one side, see if that evens it out some.