When shooting a holy grail lapse I'm still getting noticeable jumps on my final output. See the video here http://youtu.be/VBf77ymSsPw

I'm shooting with a manual lens so match total exposures doesn't work. I tried to go in and manually match the 2 and 3 star keyframes but I must've done it wrong.

When is the correct time to correct the 2 and 3 star keyframes?

You can use the lens tagging feature in LRTimelapse 3 (Metadata/Lens Tagging) to fill in the Aperture. After that you can use either the Holy Grail Wizard (check the Holy Grail Tutorial in the Tutorials section) or "Match total Exposure" in Lightroom if you want to do it manually.
The former is my advise, since it is much easier.

But apart from that: for a sequence that is so overexposed, the result is pretty good. Please try to avoid to overexpose when shooting the holy grail, because clipped highlights will be mostly impossible to match accurately.

I have been using lens tagging and I still get jumps. When would be the best time to match two and three stars manually?

You can match them manually, if you feel you get a even more accurate result then. Do this at the very end of the HG-process, then apply the "Auto Transition Special" again, this time with "**/***"-Option. Save and render.