Jason,
Not to add salt to the wound but just a few observations, sugestions & solution.
Just for the record, the CI 240 swingarms i have seen have that part of the casting completely ground off to clear the tire/wheel so it isn't an issue with their widened arm. Just so you know [

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IMO, if you have a good pedal on the lift and bad when you lower the bike and move it then i suspect the rotor is collapsing the piston which will result in a low pedal.
Anything else done to rear wheel?
A means of trouble shooting this scenario is removing the caliper body and firmly blocking the piston/no deflection so you can apply the brakes off the bike safely.
Be sure that all the caliper components clear the swingarm to accommodate the belt adjustment and future pad wear.
Regarding the banjo bolt surface and mat'l removed, if it doesn't leak it's fine, no problema!
Edited:
It looks like you need to remove more metal from the inside of the swingarm to clear the hose. As i stated earlier on the CI 240 wide arm it's ground flush to the extruded rectangular tubing on the right.
The caliper needs to be able to float and self center over the rotor at all times else you're flexing/bending the rotor if the hose or caliper body comes in contact with the inside of the swingarm.
I hope this sheds some light to the subject
Good Luck