Hiccup at 60 and when shifting into 2nd

I'm on my second (and lesser) TDI. This one is a manual 2006 Jetta. It's got 96k and it's got these two nagging issues. Sometimes it feels like it might be slipping or hesitating going into second gear. It is intermittent. With this few miles, I can't imagine it's having transmission issues. Oh, and clutch replacement by previous owner... possibly a recall thing. Any ideas?
On a possibly separate note, occasionally when I am cruising in 5th at 60-65 mph (common commute speed in the SW) I will feel a slight hiccup.
I haven't been able to nail down any specific weather, engine temperature, fuel, factors on either of these issues. I had the fuel filter changed in April with my 85k TB/pump replacement and was hoping that would solve it. Alas, it's back and very intermittent.
The second gear issue happens more often. Once, about every other time I drive it. I have the OBD II for it. I just don't know if it can help diagnose this issue.
Any help is appreciated!

Have you changed the transmission fluid? If yes, with OE or aftermarket?

After reviewing some mechanic docs, I don't think it's had its transmission fluid changed. It says "sealed" on my last oil change docs. Honestly, I didn't know that manual transmissions HAD transmission fluid. Is that a regular maintenance thing that I'm unaware of?

The transmission fluid should be changed every 100k. Takes just under 2L of fluid. I suggest the VW fluid, but there is a thread in Fuels and Lubricants that you can read. I have found the VW fluid to have notchy shifts when cold (winter cold), but shifts fine when warm.

If you change it yourself, follow the DYI that can be found at myturbodiesel.com. The fill hole is lower than the full level of the transmission, due to the transmission installed rotated toward the front of the car.

You drain the fluid from the bottom drain, and also pull one of the gear shift selector pins (after locking the gear selector), replace the selector pin, and the drain plug, fill the trans using the side fill hole, then continue filling the trans from the reverse switch hole. It is all explained in the DYI. If you have a shop replace the fluid, be sure to provide them with a copy of the DYI if they are not familiar with the process.

If you do not get the 1.8/1.9l of fluid replaced in the transmission, (equal to what ever was drained out), the transmission will get damaged in short order. I think that I overfill using the reverse switch hole by a little, just to be safe.

I recommend 50K intervals. That stuff is beyond nasty by 100K. If you have ANY sort of leak at the axle shaft seals you can get some serious contamination of the fluid as well. Fix the seal issue and replace the fluid.

As far as the hickup who knows. Could be electrical, could be the injectors. If its really ramdom i'd be looking for broken harness wires. Please have a shop do this if it becomes worse.