T5 shifter doesn’t fit?

First time poster. Thank you for any help you can provide.

I finally have my drivetrain in the car and think I have an issue with fitment of the transmission.

I have a complete Type 65 kit using a donor driveline - 331 stroker, T5, 8.8 rear end. All came from a running and driving 91 fox body.

The motor and tranny are mocked in place with all bolts fitting. The driveshaft supplied (#60454) fits properly into the transmission and will have proper clearance to the rear yoke. The two issues are:

1. The transmission mount plate only lines up with the tranny mount holes in the forward orientation, what the manual shows as the orientation for a Coyote with TKO. Probably not a big deal?

2. The bigger issue is that with everything sitting where it should, there's no way the shifter will fit as it is blocked by the cross brace across the top of the tunnel. Even if I put it back on before lifting the tranny to mount the plate, there isn't enough clearance under the cross brace. Please see attached pics.

I'm pretty mechanical but this is by far the biggest automotive project I've tackled. I've been taking it step by step and am starting to realize how much I didn't know about transmissions, tail housings, shifter locations, etc. I'd rather have a front/mid shift location but I kinda like the look of an exposed relocate linkage anyway, assuming I can get this thing mounted.