Fractured Fibula-Super Sensitive and Painful When Wearing MX Boots. Any Suggestions?

If you have any metal still in there and that doctors say it's OK to take it out, do it.
I have experienced it twice (in the same leg, 30 years apart), believe me, it works, no brainer.
If you don't have metal in there, probably a nerve has been damaged by the broken fibula and when you compress the whole area, it's reviving the trauma, not sure if there's anything you can do in that case.

I agree taking metal out if possible helps. If not try two socks on that ankle to pad it some. I have done both on mine to help pain related to bad fractures.

I have bad ankle suffer same pain. I use Astars tech 10 .
The inner booty is great. Zero pain with that setup

I crushed the top of my tibia and fibula at the knee and most of the pain was from hardware. Its no good in a joint. So x100 on getting the hardware out if possible. Also look into Sg12 boots. Very roomy and good padding inside.

Depending on where and what type of pain your feeling might depend on what type of boots you could look into. I am a believer in the Tech-10's with the inner bootie. The nice feature is with the bootie, it can be easily removed and a custom brace will fit in its place. Have you looked into any type of orthotic or custom ankle brace? Maybe your wearing one now for your daily activity?
I have made multiple custom items for riders with ankle and foot issues to help alleviate pain while riding. I always suggest the Tech-10's for that reason. I will admit they are bigger and more bulky but I feel you get used to that in a few rides at the most. Please feel free to DM me if you have any questions about what options you might have to help your issue.