Fox T5 swap

So im in the middle of doing a fox T5 swap into my 94 Cobra. I have hit a major issue. I'm trying to bolt up the cross member, but when I lift the tranny enough to line the bolts up, the shifter hits the floorpan! Has anyone here ACTUALLY done this swap?

Is there a way to fill the trans, other than through the shifter base?
 
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I didn't do an sn95 car, but I did a t5 swap into my 93 and the shifter hit the floor pan as well. It hit's it towards the back of the shifter opening. I think the AOD & t5 openings are different. First time I just used some tin snips and cut the pan opening a little larger. The t5 rubber gasket plate that's on factory 5spd cars still fit and covered it properly.

The second time I did it I just used a dremel to cut it slightly larger. Just trim it up.
 
The transmission isn't actually designed to be filled through the shifter base, it's just a super fast way to do it. You need to buy a transmission fluid pump. They are like $6 at any autoparts store. It attaches to the bottle of tranny fluid and has a plastic hose that you stick in the fill hole on the side of the transmission. You pump it up and down and it fills the transmission. It actually goes a lot faster than it sounds.

Kurt