Well, after my issue stated in the post above I gave up for a bit and came back to it after about an hour. Low and behold the screen powered up fine complete with picture (always a bonus).
Strangely, the picture was not quite as good on the 12.1 inch display as I expected almost looking slightly too dark and at an odd resolution. Quitting out of RetroPie with F4 and the onscreen text is almost unreadable.
Is this a resolution setting that needs correcting on the Pi itself or would it be worthwhile to just format my SD card and do a fresh install?
My other issue since this update (and this is a big one) is the sound. Since fitting the newer screen ALL sound has now stopped working through the speakers. I’ve checked the wiring and everything seems to be secure but the side volume control buttons have no effect at all.
As no fitting instructions come with the 12.1 inch screen, I only used the photos shown on the store page for the screen and am assuming they are correct.
I really hope someone can do a detailed step by step guide to upgrading the PiCade screen for us noobs as it would be SO helpful and eliminate the guess work and head scratching.