Your symptoms sound like a less severe version of the way my old '89 Tracker behaved when the clutch "blew up" in it (yes, those were the shop's words).  We never knew for sure, but the throwout bearing was the prime suspect in that episode.  Anyway, after it pretty much destroyed itself, it wouldn't disengage even with the pedal ALL the way in.  I had to push the stick toward 1st gingerly and kind of milk it to get the synchros to slow the input shaft down enough to slip into gear.  Then it would make horrible noise while the clutch plates rubbed against each other and the other loose parts in the bellhousing.  Luckily, I only had to limp it a mile or so to the shop that way.

So, I guess I'm agreeing with others here that the clutch is probably the issue, not the transmission itself (yet).

Good luck . . .

It might sound strange but it is entirely possible for a clutch to blow up or explode (the usual term is grenade), and if you're nearby when it does happen, it can be fatal, because the end result is flying shrapnel, pretty much as happens with a hand grenade - there is a lot of centrifugal force involved when you have a clutch let's go at high rpm, enough for the pieces to come through the bell housing, through the floor, and if you're in the way - well...

So, I guess I'm agreeing with others here that the clutch is probably the issue, not the transmission itself (yet).

Good luck . . .

Definitely what i was thinking. Once I'm underway the transmission shifts fine, and makes little to no gear noise. Repairing or even replacing a clutch assembly is something I've done before and is much easier then diagnosing and repairing transmission issues.

For now, I'll just continue to live with the clutch problem. I'm currently also fighting with EGR codes that won't go away! Hopefully my clutch plates and throwout bearing can survive another couple of months until i have more time and resources to focus on that particular issue.

Thanks for all the suggestions guys!