Paul,
Protrack will not improve your polar alignment any further - that is not what it is intended to do.
If the mount is setup fairly accurately and level (use an inclinometer on the PME base and on the OTA) then with Tpoint you should be able to get a very reliable polar alignment in 2 rounds of 6-20 points
The first run is the rough run - just do 6, 7 or 8 points depending on how close to the SCP you are and how good the sigma is
Make an adjustment and repeat maybe going to between 10 and 20 points.
This usually provides sub 10 to sub 20 arc secs accuracy and this is in the field on a portable pier.
With just 20 points your pointing accuracy should be within a few arc secs across the sky.
This will be good enough for almost any level of work.
If you have been getting large Sigmas ? then maybe that was an indication of the additional mechanical problems that your particular mount has and maybe that is why you needed 100 points to get some averaging within the mechanical errors - because there is no normal reason to need 100 points purely for polar alignment.
Read this
http://www.bisque.com/tom/Paramount/...djustments.asp
The Tpoint manual tells how to set your mount to the refracted pole (instead of True pole), there is a few pages covering this topic in two sections.
So you must have skipped over those 2 sections 10 times

- try searching for "refract"
To get better results and start removing any extra mechanical errors then you do of course need more points for Tpoints statistical analysis engine and Protrack wants lots of extra points too.
My comment re PE was in relation to Greg's question where he asked . . "Or is it not worth it as the differences are so fine that it is lost in PE anyway?"
Why on earth would you even attempt to drift align a P-ME ?
Surely that defeats the whole purpose.
Rally