Mysterious T5 transmission woes

I had help rebuilding this trans 15k miles ago with the ford racing M700 synchro rebuild kit. No shifting issues other than a slightly worsening roaring when the clutch was applied so , I had to replace the trans nose cone and throw out bearing just 6 months ago to correct the noise issue. After reinstallation suddenly second gear keeps popping out ? I triple checked shift boot clearance, shifter stop clearance and powertrain alignment (mounts).
Is this a terrible coincidence or did I mess up by not checking end spacing prior to nosecone reinstallation? Could I have done something inadvertently when I replaced this part to cause this issue ?
I called ford racing tech line and they suggested that I remove the nose cone and check bearing clearance ??? Or “end spacing “. Not a trans guy so not sure what that means or if it’s even relevant
Btw’ this car is not raced or driven hard. It’s a daily.

Thanks

Edit : the car came with a steeda TriAx short throw shifter and the problem was present until I serviced the trans the first time. If this makes a difference ?

jozsefsz said:

I've always considered the replacement of the front bearing retainer a bolt-on operation.

Mustang Improved T5 Steel Bearing Retainer (83-93) - LMR

Replace your worn out 1983-1993 Mustang T5 bearing retainer with this all new and improved steel bearing retainer from 5.0 Resto!

lmr.com

Following the procedure in this video, the only thing I could think could have resulted in a shifting problem would be if you torqued it to 500lb-ft or something, or perhaps left out the shim from the old nose-cone when you installed the race in yours? That could potentially cause enough slop in the transmission to make it slip out of gear.

Click to expand...

Thanks. Either way I’mma have to R&I this unit again.