Okay been working on this this morning. Focusing foremost on the fuse 'box'.
For a start the battery is in good condition. Bearing in mind I ran last night with the lights on the standing voltage when I measured it this morning was 6.25v.
I did some tests with the multimeter:
battery 6.25
idling no lights
6.15 at battery, 5.98 at fusebox (loom side)
w/ lights
5.85 at battery, 5.25 at fusebox (loom side)
Then I did a bit of rigging of wires to essentially bypass the fuse/box.
And got the following:
idling no lights
6.15 at battery, 6.15 at fusebox (loom side)
w/ lights
5.75-80 at battery, 5.75-80 at fusebox (loom side)
So it's obvious there is significant draw at the fuse box, the fuse connection, or wire connections. It's worth noting that the charge light only glowed at idle after rigging my wing. Unlike before when riding the charge light would be glowing very dimly (w/ lights on, even before this stalling issue occurred more often), giving the bike a small rev the light immediately stopped glowing. More so, the intermittent 'missing' seemed to disappear too so definitely on the right track to start with.
So, I've cleaned up the spade contacts and crimped down the connection tangs slightly too, but additionally also changed outright the positive wire spade connection on the loom. The fuse box itself isn't in good condition with broken connection tangs (no earth fuse, battery is directly connected to loom) and also split sections too- so need to replace that (always intended to anyway actually). I've cleaned it up as best I could and tried to solder the cracks in the metalwork but that's the best I can do for now with this box, anyway. But for now the bike is back together with the fusebox and everything connected.
After all that I get 5.75v @ idle with lights at direct connection (bypassing fuse). But through the fuse box 5.65v. It's also worth noting that fuse orientation can also reduce this to 5.55v.
Bike doesn't seem to misfire at idle or stall, at least whilst in the garage. The real test will obviously be to use the bike when I can and return my results and then if not favourable continue with my diagnosis.