Thank you everyone for your input. Going to have another read through it all and properly process it when I am not dog tired!
In the interim however, I did start off with using EQAlign as a way of doing the drift alignments. Free software and it does work really well, doesn't have the "real time" feature that PemPro does but it works well all the same. I have seriously considered purchasing PemPro and may still do it in the future, even if just as a way of getting some damn good PEC curves
I do agree with the sentiment that I am probably going a little over the top for a lowly EQ6 Pro
It doesn't have the most accurate encoders, many seem to suffer with backlash (although I haven't really noticed any yet with my limited usage). Not say it's not there, just haven't pushed it far yet.
There are a couple of reason I did choose to go down the path of TSX over PemPro for alignments though. Using TPoint takes an all sky model, takes refraction out of the equation. For a temporary setup it is debatable as to whether the difference is worth the effort, I do agree with that. For what I am planning on doing, I do need pointing accuracy though. When I get everything up and running I plan to start doing astrometric studies on a few dozen globular clusters over several months. I have an interest in RR Lyrae stars and want to do some research into the variability of variable stars (they have a ~40 day cycle). This involves slewing from one cluster to another, taking one image and then moving on. Accurate pointing makes my life much easier to say the least.
I am also planning on having a semi-permanent setup both at my house in Melbourne and my dark site in Heathcote. When they get established, having strong TPoint models already done means I'll only have to do a resync to them, 15 minutes and I am up and running
Right now my mission is to work on one aspect at a time. First it is getting to know TSX, then auto guiding, then sequencing. Sequencing will probably be done through SGP running with TSX for mount control. As much as I love MaxIm, I haven't sat down to learn Visual Basic to write sequencing scripts for it yet. Maybe in the future!
I know that within about 40 minutes from power up I should be able to be pretty accurately polar aligned (enough for me to be happy with a temp setup), have a 60-100 TPoint model and be ready to go. I have a digital level which gets me quite easily to within half a degree and I am looking at making a mount attachment for my compass to get me within a degree from cold setup.