Well, a new tranny is the last resort. I am having a similar problem Could be bad Synchro's as a result from wrong fluid(not using nv-t350). Or you could be looking @ my problem which is the Clutch Housing Bearing. Did they replace the Clutch and the Throw Out Bearing?? There are many things is could be but my money is on Wrong fluid ruining your synchro's but really the Clutch Housing Bearing. Ill post the PNC number later.
314 226 3776 you can call if you want and i can maybe give you a run down.