99-00 are a lower torque rating that the 01-03 for the 7.3's. The 6.0 and 6.4 trannys have a bigger pilot bearing shaft than the 7.3, but I'm not sure if they upped the torque rating from the later 7.3 trans.
The output spline shaft is 27 on the 7.3's and I think it's 31 or 35 on the 6.0s. Also the bellhousing is different. I think they may have made more 6.0/6.4 trannys which could help with availabilty.
