Hi Dave
I am not sure what might be causing your computer to stutter/wobble. It might be the machine not being able to cope as I am not sure of the spec of your machine. I do have one suggestion though concerning the guitar track. The wobble might be due to the bpm detection engine in TrakAxPC ( very hard to know without actually seeing the issue myself)
When you record the guitar and place it into a track in trakAxPC, click on the bpm parameter button on the track. I have included a screenshot.
Once you click on the button, in the stretching engine section select high quality (see screenshot).
When you select high quality, click close. One word of note - doing too many tracks at high quality can effect the performance of the application.
I am not sure if this will fix the problem but it could be worth looking at.
I hope this helps and fill us in how it goes.
best regards
Cormac