A "shifty" manual transmission issue

Hey gang-

Long time thread reader and lurker and now I've got an issue that needs a little more guidance.

My truck in a 2006 with a 6-speed manual and 4wd and resting at about 93k miles.

A couple of months ago I had my clutch and throw out bearing replaced at a local shop. After driving for about a week or so, I started having some trouble shifting smoothly into 1st and 2nd, especially in a lot of stop and go traffic.

Coincidentally, the truck noticeably idled a noticeably rougher directly after the clutch replacement; I'm not sure if they are related or not, but perhaps worth noting.

I took it back to the shop where they adjusted the clutch and ran some fuel system cleaner through. The truck did idle smoother and having the clutch adjusted helped with gear changes but it didn't seem to clear up the issue entirely. The shop was unable to replicate any problem, and honestly, there doesn't seem to be any reliable time or scenario that it acts up for them to witness it.

The issue now is that the truck can at times be difficult to take out of reverse and occasionally shifts hard into 1st, 2nd, and 4th. Some shifts it's smooth and normal and the next time through gear changes it takes a bit of wiggle or second attempt to find home. Then it's ok again. No rhyme, no reason.

No clunking with shifts, no vibrations or sounds to note. Clutch travel is smooth and easy. No other outstanding things to note.

Any ideas from the masterminds here?

Thanks team!
Lee

 

Bleeding the hydraulic clutch system would be my first step, if that hasn’t been done already.