Hi Alex,
Let me try your subs with CCDStack.
You can use
www.yousendit.com to transfer the files to me. My email is rat156 and I'm with bigpond.com
That way I can try to use CCDIS to align your subs. I'd like to know if it'll work, if not the Registar is the way to go.
WRT refocusing, the only problem is that your red stars may be smaller than your blue and green, this is not uncommon with refractors I believe. Check the FWHM of a star in you images, make sure it's not saturated though. If the red ones are significantly smaller then you will have to refocus between colour subs or find a "sweet spot" for the colour. Remember that the RGB subs aren't quite as critical as the Luminance wrt focus. In fact as you will probably be binning them, I'd put a little blur on them before combining them anyway (reduces the colour noise).
Cheers
Stuart