Brett,
If you're still persevering with PixInsight the process I'm using is:
- add panels together one at a time using StarAlignment Register/Union mode and Frame Adaption to create an initial rough mosaic
- register each of the panels against the rough mosaic using StarAlignment Register/Match mode, using Frame Adaption again
- Assemble the final mosaic from the registered panels with GradientMergeMosaic
StarAlignment will use previews to restrict the star matching process so you can use this to provide hints where the joins are to expedite the matching process.
If your linear data is good quality then just stitch the panels for each filter together and do the stretch and other processing afterwards. If the quality is not so good you may need to stretch the panels and possibly do NB/LRGB combination first.
There are more exotic techniques and tools for wide fields, distorted images, mosaics with gaps between panels, etc.
Cheers,
Rick.