Trouble with DSLR workflow to align and generate 2 seperate integrations of Ha and RGB

I'm curious to know what is the correct workflow for generating 2 seperate integrations of data taken with my DSLR on 2 different night using a 7nm Ha filter and my L Pro filter? 

My end goal is to have 2 separate and aligned integrations of my Ha and colour data for layering and further processing in pixinsight and photoshop. My data was capture using as astromodded Canon EOSM100 with stellarmate, with picture files saved as RAW fits

I have looked through the forum and tried many of the methods mentioned in a few places without much success... and I'm just going crazy! Probably spent 2 days trying to figure this out so far...

This is what I have tried:

1) Did a full integration of my Ha data using the Hydrogen Alpha algorithm in the 0) RAW/FITS, integration looks amazing  then in a completely separate session I tried to use this Ha integration as a reference frame to align my colour data too it, deselect the Ha before integrating.. Java error.. remove the ha frame from the session, integrates fine

2) Tried to integrate my colour data and only import the Ha frame that was used as a reference in my Ha integration session instead of the full integration so the picture size is identical, go through all the steps, set the Ha as reference and deselect it before integration...  java error when integrating... remove the Ha ref from the session altogether, RGB now integrates perfectly, looks great but not aligned to my Ha integration as a result...

3) Tried loading all the files together (Ha + Colour) in a Multi-Chanel processing session using the "Supported/ adaptive edge" Bayer array, Assigned Ha to session 1, RGB to session 2 and go all the way through registration, output each session separately in the 6) Integrate tab. Everything is lined up great but my colour integration is horrible with a massive blue tint all across the picture... the Ha is ok but again nothing compared to processing Ha on its own using the Hydrogen Alpha algorithm

4) Tried loading all the files together (Ha + Colour) and go all the way through registration, saved registered files and then integrate the exported registered Ha and colour data separately in 2 completely separate session, that works in terms of all the shots being aligned... the integrated RGB comes up great but now when I integrate the registered Ha data in a seperate session using the Hydrogen Alpha algorithm in the 0) RAW/FITS it looks no way near what I got when integrating my original Ha fits files. I have noticed that my unregistered original files show a CFA of RGGB, but the registered exported ones shows a CFA of "No" which seems to be the culprit as to why its not working the way it should...

5) I've tried to change my integration mode in 3) and 4) to  "Reference" mode in order to keep all the frames at the exact same size to see if this would avoid me getting the Java error... but nothing...

Any idea? Thanks in advance for your help and advice.