Largish update:
When I mentioned about if the system had two sets of batteries instead of three to make the wiring easier, I meant the one on the second down on the left side and the orange on on the right side. This would allow for better wire bunching and less wire cramming, not having to be concerned with one of the capacitors laying on top of the right orange battery making it necessary to move the wiring around it, and also on the right battery, making it harder to get the extension plug (more on that in this post) in place. In saying that, although it would have been a bit easier with two sets instead of three sets, having 50% more playtime on a battery charge is a nice prospect, so worth the extra hassle if you can manage the tight spaces.
It would have been better to also have angled the right orange cell closer to the memory card compartment; but as it has a little hot glue keeping it in place, too late to bother with.
Moved the 3amp wire about as otherwise the board won't lay right against the cells.
Dremeled down the power plug for the CD drive and the data lines plug for the CD drive as they were pressing against the memory card holder, anyway, no space to have a port attached. Needs to be wired directly.
Two methods to do this wiring:
Method 1:
I tried this out, had two rogue connections on the CD drive cable, one I managed to resolve but the second one was being a pain. I ended up removing the CD mechanism, painting the top of another one and installing that into the system again, and therefore using method 2 (below). Up to you which one you try, Method 1 is fiddly, however with method you you will need to destroy a second PSone console mobo for the plug; or, if you are nimble enough, removing the plug from your board and not needing a second board.
Method 2:
This is the plug we need to relocate.
Decided to just destroy another board. Extravagant but I was a bit frustrated at this point having spent a while trying method 1 out and failing.
Pry off:
Made the extension cable:
Wired up the memory card. Used the wiring again from the PSOne console cable, convenient.
Also wired the positive wire from the battery packs to the switch; and also wired the L2 and R2 shoulder buttons.
This is what I meant about the benefit of not having the right orange battery - managed to squeeze it in though, barely.
Rewired the CD drive power (the 4 wires) directly to the board, and also pushed the wires from the memory card through the console board. I have a small space between the battery and the edge of the case so I can push the wires back through. Again, if this battery wasn't here, wouldn't have that issue!
Wired up headphone jack.
Important to cover any metal or contacts with electrical tape to prevent shorts.
I was going to wire up a spare PSone screen to the system to test, but thought it wasn't time efficient to do this, so rigged it up to the system case instead. This means I am playing Russian Roulette a bit, however if all works fine as it should, I will be close to completion.
Wired up most of it now, have the shoulder buttons, power, headphone jack and the controller to wire up yet. Apart from power, I will add these other items for final wiring until I know the system works fine.
Not going to try the system until tomorrow, gives me a chance to check things over before I test the system for any obvious errors. Time is short today anyway, need to go to work fairly soon.
This has been a massive project and involved a lot of modding work, some I have tested, some is untested. I am just hoping that the important things work fine and I just have tweaking to do and a bit of tidying up to do. What I don't want is a blank screen and smoke - worst case scenario!!

I have more confidence in my work than that, but let's face it, we all have that fear before first switch-on - you know if the months you spent working on a project is a blazing success or resounding failure!
Oh well, wish me luck for tomorrow! If all works fine, I will have the project completed before the end of the week. If I have problems, who knows...
Not had rumble motors yet from the USA delivered, so that is another thing I need to complete, also want to have a crack at Mario's low-battery LED mod too. These are the last parts of the work to undertake, neither will take more than minutes to do - I will test Mario's mod with AA batteries as I have many of them and they are at slightly different voltages, so by changing one or two cells I can test the LED at 6.9v - 7.5v to make sure it does what I want; ideally, I want the system to light the LED at 7.2v or 7.1v as the screen dies at 6.89v.
Oh, just as I was typing this post, postman arrived - got my rumble motors from the USA, as well as the 1 watt resistors; yesterday I got the transistors and the LED's. This means I have the extra components!!
The rumble motors aren't that powerful, but anyway, how can they be - they are only 21mm long end to end. They do rumble ok though and they also make a noise, so the combination of both factors should be adequate: anyway, no space in case for bigger ones.