2003 double cab 5 speed swap shifting problem

so i guess ill start off with a little background. me and a friend are having transmission shifting problems in 5 speed swapped double cabs. what its doing is once the vehicle is stopped you can still hear the clutch spinning every so slightly, making it hard to get into first or second or reverse. if you can get it into first before stopped your ok, but if you try after stopping you cannot get it in unless you work it into 5th gear and then you can hear the clutch stop and shifts smoothly. always shifts smooth driving around town or highway, only has a problem when stopped. problem only starts after a couple thousand miles on a new clutch, after that it show the problems.

mine is a 2003 prerunner thats been converted to 4wd and later 5 speed with a gear drive gase with 4.7 gears, and inchworm clockable adapters to the stock tacoma j shift chain drive case, a lc engineering stage 3 clutch, new aftermarket flywheel, lc engineering short throw shifter, all 5 speed donor parts came from a 1998 4runner i bought and and parted out
second is a 2001 double cab that was factory 4wd, converted to 5 speed, has a gear drive case and all trail gear adapters to the stock electric shift tacoma tcase, had a centerforce clutch and now a marlin crawler clutch both with the same issues, has rebuilt the transmission hoping to fix the problem, added lc engineering short throw and still has issue

just curious if anyone else out there has had the same problems?? tried doing all kinds of researching and measured everything on a factory 5 speed tacoma of a friends that we put dual cases in and waiting to see if he has shifting problems, all measurements look the same on all 3 vehicles. i work in parts at my local toyota dealer so i have checked with the mechanics, had a couple ride with me, and looked up what i could in the fsm's that we have. thanks in advance!