So yes, I had this issue with my steeda strut bar, which has even more room than a Ford bar. It actually rubbed on the LHS or on the inner fender depending on the position of the CAI tube. The Steeda brace has a kink that allows extra room for the tube, but still had the other issues.
I corrected by adding a pep boys special, rubber coupler. It still was a struggle to put on and probably should have just left the stock intake tube as it didn't look that bad and prob. doesn't add much in the way of power. So with the ricer coupler it doesn't rub on the inner fenderwell or the strut bar. See below for some pics....
Added height of stock vs. TF plenum:
Stock CAI tube connected to 70MM TB and TF plenum (works fine):
JLT CAI with ricer coupler (before I added an open filter)