I keep getting a low battery after the car is parked for a few hours but its very inconsistent, sometimes I'll have the car parked overnight and be fine and then the next day it'll be dead after 4 hr. Lights, gauges and intercooler fan all turn on but there's just not enough juice to turn it over!
 
The alternator seems to be fine and I've obsessively checked for any lights that might be on in the car and fans staying on after the turnoff and nothing there. I had a brand new battery in my other 2 so I whacked that in and that made no difference so its not a bad/old battery either.
 
Does anyone have any ideas for a likely culprit? I plan on borrowing a multimeter and testing circuits fuse by fuse to try and find where the drain is but if there are some common problem areas anyone knows I'll test those first.
 
The car is a 1990 SW20 Turbo, has a modified sound system with two amps, one running the speakers and the other the sub (I think, came with the car so I don't know much about the install) some gauges and an Apexi Power FC. The sound system is off, so head unit and amps don't power up and that didn't change anything, the gauges do require power to remember if warning sounds have been switched on or off but I doubt that enough to run down the battery. Apart from that no other mods involving electrics except for LED bulbs in the interior.
 
I drive around with a spare battery all the time now and give myself a jump start from it a few times a week which is a pain in the ass haha!
 

This may sound like a silly suggestion, but when I first got my SW20 there were a few times when I thought I closed the boot properly, but actually I didn't so the light in the boot drained the battery after a few days.
If the latch makes contact but doesn't close properly, it makes a similar sound compared to when it does close properly (because the boot lid is so light). One day when I was driving, the boot lifted a bit when I hit a bump, and I immediately realised what had been draining the battery! Epic fail on my part, but worth mentioning haha.
 
Apart from that, it sounds like you've already checked a lot of things, so it would be a good idea to use a multimeter and pull fuses one-by-one, as you mentioned. You can set the multimeter to measure current, then disconnect one of the battery cables and put the multimeter probes in series with the cable and the post on the battery. Then you will be able to see how much current is being drawn with the car off, and see which fuse/s need to be removed to reduce the current to an acceptable amount.

Haha yeh i thought of the boot light, even shut it with my phone in there recording video to make sure it turned off properly! But it worked fine so the search continues :(

Do a You-tube search for videos for finding power drain sources. There are some good videos on how to systematically eliminate possible reasons for this happening until you find the culprit. It might help you in tracking down the fault.
cheers
Steve
 

I had a problem of my battery going flat over a few days and it turned out to be some thing really simple.
 
My ignition key was worn allowing me to remove it from it's barrel and still leave the accessories (digital clock display etc) turned on.

I always had similar issues but was 2 days>flat batt.
 
When I did my rebuild I took part of the alarm out as I found corrosion on the wiring.  Never had a issue since.  Any chance you have an AM alarm?

Found out the cause is the power windows! The motor intermittently keeps running which was why the battery would only run low sometimes. I haven't had a proper look at it but pressing the window lock has fixed it for now :)