I suppose it is necessary to update this post so new people reading know what's been tried etc. From the beginning:

1. New radiator. Beams engine swap. Radiator plumbing maybe sub-optimal, but it works. New thermostat.
2. Rusty coolant from swapped engine. Temp gauge erratic. Proceed to flush the coolant. Tested thermostat (submerged in hot water) - measurement within specs, working fine. Instructions for flush/bleed/refill is followed religiously from BGB and Reddtarga (MR2 Veteran).
3. After refilling the coolant, engine slowly overheats after getting up to optimum temperature. Radiator cold. Let car cool off for ~10 mins. Drive car hard. No problems. This scenario repeats at least 3-4 times, after refilling coolant. Changed to genuine thermostat. No difference. Give up.
4. Take it to mech. Report: Thermostat opens very slowly - only after 10-15 mins. No overheating episodes. Temp sensor tested and it works fine.
5. 20/10/12. Temp erratic again. Raises fists to the heavens.

Today:
After heading home from church, temp spikes. I pull over. Radiator is cold. Wait for the car to cool off. Temp gauge erratically comes down a few times. I turn ignition to ON and off several times and notice that each time I turn it ON, the temp reduces lower and lower until it's above cold the mark. This indicates that the thermostat is slowly opening while the car is cooling down. But this is nothing new. The only difference here is that it spikes instead of gradually overheating. I drive home in peace. Radiator is now hot. 
 
So the big issue/symptom is that: Thermostat opens very late - ~10 mins


In conclusion here are the potential problem areas and solutions that I think most of you will agree to:
Head gasket - not providing enough seal to pressurise coolant in the system. Once the thermostat is open however temps seem to stabilise. Mech says there's a potential this is the issue if driving it hard causes temps to rise.
Solution: Cooling system pressure test. I think before spending any more $$$ this is the way to go so as a logical process of elimination so I'll know what to do next. I'm broke anyways.
Coolant plumbing - engine was swapped by incompetent mechanic. Water plumbing maybe not the best although I'm not sure of the specific symptoms. Solution: Change all pipes hoses.
If a mech (specialist I might add) couldn't get rid of simple air bubbles what makes you think that air/bleeding is the problem?
So yeh anyone who says "you didn't refill coolant/bleed air properly blah blah" I'm just gonna ignore but don't take it personally now that you understand where I'm coming from. Actually it's probably better I ignore rather than respond in an aggravated matter
 

As a side note, where did you source the beams from. Any warranty?

Yeh the water pump idea has been brought up before. It was replaced when the engine got swapped in but I'm not sure whether it was genuine or not. But changing the water pump = taking the engine out = $600 already  . Do what you gotta do I guess
 
Engine was from SSS Automotive, it was quite a clean engine all three mech's agreed. Done under 100,000 (claimed 70,000). 2nd Mech reckons the head got re-coed sometime. Whether it was due to past overheating in Japland or not is anyone's guess. Warranty was 1 month after they sent the ECU. It was finished months before the engine actually got fitted LOL
 
Mann...getting the engine out again I may as well pull the brakes and put in redtop extractors, LSD...
 
 

Engine doesn't need to come out for a water pump change does it? A timing belt can be done with the engine in.
 
Edit: Can you find out exactly what type of water pump was installed?

Mrskylighter

Engine doesn't need to come out for a water pump change does it? A timing belt can be done with the engine in.

Correct.

lol only if you live near me ... i would have lend you my creeper :)

Mini update
I spoke to the mech who swapped my engine he's adamant that the water pump is correct and I believe him as he sounded quite honest (even if he made past mistake). The brand of the water pump is Repco, and he's never had issues in the past.
 
I then spoke to another mech who reckons that my car is missing some sort of bypass hose which would be the reason the coolant doesn’t reach the radiator. Makes sense. If this is the case my initial assumption is correct >:D and I’m the unofficial MR2 water system pro (not really)
 
Booked in for a coolant pressure test (called it a decay test?) anyways to check head gasket integrity.
 
I’m also in for a dyno run this Sat so wish me luck the car doesn’t overheat on the rollers lol