Sorry I'm late to the party. I've done 3 6060/rst or rxt swaps recently and the two with stock TOB's which didn't use a shim, the other was with a Quicktime bell and a tilton TOB. From my own research and from McLeod tech it only takes .325-.350 movement to fully release the street twins, while our stock TOB has a throw of .440-.460. has it been verified that you are getting over .400" of throw out of the TOB. If not you could have air trapped in the TOB. If that is the case then it should be bled, but considering I never got the ford vacuum bleed procedure to work well I came up with my own way and It hasn't failed me on over 25 clutch installs.
Its always a good idea to bench fill new TOB but have done it both ways with success.
After trans is installed and hyd. lines are connected with the m.c. reservoir is topped off with ford HiPo DOT3.
1. Lengthen (front to rear, width can be the same as stock) the inspection hole at the bottom of the trans bellhousing. (can be done before install or after)
2. With a long skinny prybar or long flathead screwdriver (even a long gasket scraper) place it through the bigger inspection hole.
3. Place tool tip between TOB bearing surface and clutch fingers.
4. By either twisting tool or pushing handle towards the front of the vehicle, push the bearing to the fully compressed position and Repeat 10 times
5. Then have partner or yourself push the clutch pedal in 10 times in a slow fluid motion (not fast).
6. Repeat steps 4 and 5 til firm pedal is achieved.
7. Have partner put trans in gear and stay in vehicle.
8. With you underneath the car, try to spin the output shaft.
If it still spins by hand , clutch is not engaging and usually needs to be replaced or rebuilt. If it doesn't spin, put force on output shaft to spin while partner slowly depresses clutch pedal. If it spins before midway down or so then you are done. If it goes to the floor before hand spinning, repeat steps 4-5.
To check TOB throw...
Install TOB, hyd lines without the trans or if ss line is long enough, then while on trans but not bolted to the engine with enough room for two sets of hands in the bellhousing.
1. Use above steps and bleed the TOB, instead of tool through the inspection hole just use you hands to full collapse the TOB (advise to lock wheels on tranny jack or hold trans with one hand while pushing the TOB in for leverage and to stop movement of trans.
2. After bleeding the system, check by letting the TOB be in relax state, have partner slowly and lighly press on the clutch pedal (WARNING don't press hard or seals will fail) If it is rock solid then its time for measurements. If clutch pedal moves more than just the free play then keep on bleeding.
3. For this step only, have a third person get in the driver's seat (simply anyone that can push a clutch pedal to the floor on command, ie wife, gf, son, daughter, grandma, etc)
4. Using a dial indicator, digital micrometer, or anything with accuracy better than .010", with one person depressing TOB full collapsed, measure from top of TOB bearing surface, to a repeatable surface (for example the TOB mounting flange flat surface).
5. Record measurements in each quadrant and average together.
6. While still have partner A holding the TOB fully compressed, have clutch pedal person full depress pedal to the floor.
7. While both partners are essential fighting each other via the hyd. system, make and record measurement in the same location in each quadrant.
8. Subtract pedal down measurement average against pedal up measurement average to get TOB throw.
If you have any other questions let me know.