I finally have success!
I gave up on my Pheonixed Progear, as that B board has issues for sure, and picked up a Gem Fighter that had been phoenixed (cheers chapddr).
It was a rev7 with GPAL - great! then I noticed that the jumpers were off, I had to desolder and resolder a few points. Oh dear I am **** at this kind of thing.

I picked up a new soldering Iron and desolder pump and got to grips with desoldering well enough, except for one point which I just could not get some residue seemingly off. The other easy task of applying blobs of solder to the correct points was a nightmare, the solder didn't want to stick to the board points - just to the tip of the Iron.

I then did continuity testing and somehow my absolutely shocking work seemed to be solid.
I had dismantled the Multi pcbs from the Progear board without breaking any pins and so I then remove the chips from the Gem fighter board (I can't believe that there were so many chips on this board (I also will never know how to put them back in the right place because I forgot to take a photo of the chips in place doh!)

I managed to connect the multi to my Gem B Board and then tested it ... only to not get it working. I checked the connections and noticed that some pins weren't in 100% and so carefully pushed them in more ... still wouldn't work.
Before i gave up and chucked the lot in the bin and had a closer look at the setup and I noticed that there was a change better or worse when I plugged in the LCB cable plug to the main multiboard and suspected that I needed to ensure that perhaps some pins were in too much, so the others were almost indecipherably off. I used a bit of magic-hands to massage the board into what I thought was a more even alignment and lo and behold it started working!

I haven't had the guts to put the multiboard back into the CPS II case just yet, I figured that I don't want to fiddle around with it whilst it is working, or I'll never get it going again.
The select button on the LCD screen came off in the post, and there is no way that I can fit a new button, so I now poke at it with the chopped off end of a Q-Tip

I'll also have to live with not having auto-reset because I am clearly a hazard when I try to use a soldering iron.
Just a few things that I wouldn't mind clarifying;
1) The avalaunch 15/05/31 pack, does anyone have a list of the full names / regions? I am not talking about fixing the folders, I just want the list, so I can learn it.
2) SSFII X I noticed that the attract mode has no sound, every other game is ok, any reason why this game doesn't have it?
3) When I finally get the balls to put the Muti back in the Case I want one of those stickers to put on the B Board (as my Gem fighter had no label anyway. Where do I order this from? I'm sure I saw a post showing them, but it's not in this thread.