I remember when you first got that sled you were blowing belts and wound up doing some motor mount replacements. Wondering if you had a torque link installed at that time? A must if not.
The most important thing on the alignment is that the crank and jack shafts have to be absolutely parallel. What makes this a challenge is the fact that the sled is not set up to be adjustable on ANY of the settings (except offset- secondary shimming on jackshaft) regarding alignment (motor mounts, plates are not slotted), and to adjust you need to get creative with shims....I wound up with shims in all but the RF corner.
Have heard since this is the way it SHOULD have come from the factory. You might want to check that it was re assembled properly when the mount work was done?
Was rewarded for this messing around big time, sled finally started coming up into the numbers I had heard it should be(115+).
Holler if I can help.