I had to replace the motor in my 95 a few years ago. As I recall I did not have to remove the glass and the entire job only took about an hour.
Are you sure you are doing it correctly? Mine was a 95 vert.
1965 Coupe 5.0 GT40 Intake and Heads, 65MM TB, chipped, T5, Shelby drop, roller idler, subframe connectors, Magnaflows, Hurst shifter, MS clutch, BFGs on 15" TTDs, Roller perches, Bilsteins, 3.54 gears, LS, Needs everything else...
"If you didn't build it; it's not really yours."