I had put in a new clutch last weekend and now I am noticing that in higher RPM's the shifter shakes and vibrates like a bat out of hell, I can definitely say it wasn't doing this before and I haven't noticed it until now because I haven't been getting on it too hard. I made sure all the mounts and brackets are tightened properly. Any ideas, tips, pointers?

 

Diff mount, motor mount, shifter pivot, tire balance, pitted axle cup, one or more of these things can be off which would cause shaking in the shifter. It does shake to a certain extent as the car goes over bumps and road imperfections, but if it's excessive one of those things listed is the cause.

Seeing as you recently did the clutch, I'm going with cracked shifter pivot. Checking everything but the axle cups is pretty quick and easy to do, so I'd start there and save the cups for last.

 

Differential mounts I had taken out about 3 months ago to replace my diff, they looked almost new. Tires were replaced about 2 months ago by myself, about 3k miles on them so far. Axles are Driveshaft Shop 2.9 with no problems, replaced about a year ago so I know it's not them. I re-greased the shifter when I did the clutch and put in all new parts (plastic pieces on the shifter and spring). The motor and transmission mounts didn't look bad but I guess I wouldn't really know just by looking at them.

 

I had a very similar problem after an engine swap and new clutch. One day I noticed a bolt under, and then behind, my car on the road. Went back to get it and found it was supposed to be holding the trans to the engine. Another bolt was completely unthreaded and hanging on by luck alone. Shop reinstalled and torqued all bolts, and that rattle and vibration is gone.

Vibration was worse just above 6,000 RPM, and worse still when the revs dropped down to that range (as opposed to climbing through). Occasionally it wasn't evident, but was there most times.

 

Pitted axle buckets cannot cause a shaky shifter, neither can tire balance, or a bad diff mount.

Motor mounts and trans mounts are number one cause.

 

Technically those things make the whole car shake. The shifter is just a casualty of the global shaking.

 

Someone mentioned if the plastic pivot on the end of the shifter rod is cracked it can cause a vibration in the shifter.

You mentioned this part was replaced as part of the clutch replacement. Are you certain it didn't become cracked when the new piece was installed? A lot of guys have to heat this part up to soften it to get it to fit onto the ball socket without excessive, crack inducing force.

 

This.

 

Billman250 nailed it. If you're not careful and your car is on the higher mileage side, you may crack your motor mounts from hanging the transmission off of them when pivoting to gain access for the top 3 bell housing bolts.