helps to state the year you're working with .... some of the trans mount bolts are accessed from inside the bellhousing, check if that's the case with the ones you think are 'broken off flush' ... your shop manual will have the procedure for trans removal, I believe with the torque tube the usual is to drop the rear loose and move it back

Bill

Moved over to the Passing Lane

"When we tug a single thing in nature, we find it attached to the rest of the world" ~ John Muir
"When we tug a single thing on an old truck, we find it falls off" ~ me
Some TF series details & TF heater pics