I have 2 garter spring from pulling the manual transmission and I can not figure out where they go with the repair manual .

Any help would be greatly appreciated.

Attached is are pictures.

 

Most likely those are from the cv axle seals. The only other seals with that size of spring seal are in the tranny which would have to open the case, remove shafts just to get at them.

 

I did pop the transmission apart to replace the counter shaft bearings. So it would be the axle seals then?

 

The larger one could be the axle seal but the smaller one is probably from inside the case. They could even both be from inside the case since you opened it. Best to open it again and start looking and find out or you will have leaks.