In the Fox body cars, as well as the classics the shifter seals all install from inside the car.  There's nothing up inside the trans tunnel. 

Here is one that was recently posted showing the factory installation.  Looks like the SN95 boot is same or very similar to the Fox.

Funny, my buddy and I were just talking about this.  He has an SN95 Cobra, I have an '89 GT.  We've know each other for about 20 years now and wrenched on each others cars quite a bit.  He got tired of breaking his T5 and swapped in a then pretty new to the world Tremec 3550.  This meant that he could not longer use his PRO 5.0 shifter, and had to buy a Tremec specific one.  When I bought my '89 he gave me his old shifter, which I couldn't wait to install.  I removed the console plate, removed the lower boot, and found that the front bolts for the shifter were so far under the tunnel that I could not access them without dropping the trans crossmember.  I didn't have a lift in those days and had recently swapped a clutch in the car and had no real desire to do the jackstand dance again, so I set the shifter on the shelf and ran it with a stock shifter.  I'm using that Pro 5.0 in my '67 now many years later, and he asked me why I never ran it in the '89, and I told him about the bolt issue.  He said that was funny because his was easily accessed through the hole.  Having looked at a lot of them over the years  he said it seemed that Ford had a guy on the line who just cut the shifter hole wherever he felt like it, and he'd seen them vary by a lot, even in shape over the years.

On a side note, never powershift a T5 with a stock shifter.  I have a second gear hanging on my wall of shame that shows what happens when you do. 

Thanks for all the responses.  I think I will go with Steve's method (sorta).  I will use the stock seal and contour it to fit the transmission hump.  I also will be using some RTV between the seal and the hump.
Thanks again, Heem