Spent quite a few days getting my Wordpress site up and guides done, so been away from this project for a little while, sorry about that!
I have only two spaces in the case for batteries - on either side of the cart slot. I could relocate some of the capacitors, but don't need to. I just bent back the fuse, diode and capacitors a bit, that seems to have made enough space. One of the two sets of two cells needs to go as per the pic below.
If I place the cells in the wrong place, then they won't fit, so to help with that, I stuck a strip of sticky foam pads (1mm thick) to the back of the batteries, put on top of the board and placed the case base on top, which left the cells in their final position. Although they are in place, and being wired, I won't hot glue the cells in place until I am happy the system will shut right.
When wiring up to a protection circuit and soldering to joints, the protection circuit can cut out power, so don't be concerned if you get zero volts. When the charger is wired up, charge the cells for a few seconds, this resets the protection circuit and allows for voltage to output as normal.
Update - system is running now off the internal batteries; the single pole double throw on/off switch is fine - thought it should be, only has to carry about .55 amps after all for the system and about 0.7 amps - 0.8 amps for the screen, when connected.