I am currently running a Gen 3 Helix 12DI, I know I can run the Mega 360 but the Mega 360 I am looking at is used and is currently mounted on a Fortrex. My question is this, does this bracket come off and can you buy another bracket for an Ultrex? Where is the best place to buy this bracket?

Yes, just remove the Fortrex shaft clamp (loosen the two socket screws), slide it off, and install the Ultrex mount.

BUT the Fortrex version is 12" shorter than the Ultrex version.

https://humminbird.johnsonoutdoors.com/us/shop/accessories/360-imaging/mega-360-hardware-kit-ultrex

Oh Damn... Thats what Humminbird was talking about then...So the Ultrex version is 12" longer?

I can use the Fortrex shaft length on my boat as well as a 45" trolling motor shaft.
I had to cut the Ultrex MEGA 360 shaft length to have clearance from the trolling motor head turning since
I have all devices as close to the water's surface as practical since I fish in trees/stumps a lot.

Measure the distance between the bottom of the trolling motor bow guard and water's surface to see if the Fortrex length is enough for you.

Ott Defoe has a video cutting his 360 shaft so the pod is submerged the least it can be for him.