So I started playing around with the controller. Initially I installed it to measure manifold pressure only from the spare nipple (without the solenoid and without capping tvsv) so I could see how it was running. I was seeing readings of 4-6 psi, with a maximum of 7.5psi wot in third. 
 
After I installed the solenoid and plugged tvsv, it was comfortably reaching 10-11psi. I still need to tune it properly and don't want to push it without a FCD but it made a significant difference. 
 
I suspect the cause of the low boost may be that a previous owner had a boost controller installed (possibly Apexi AVCR given disconnected splicing into ecu) and disabled tvsv, and then removed the boost controller prior to sale so that it was running on waste-gate pressure only. I'll have to have a look underneath to see if the tvsv coupling (blue apparently?) has been disconnected.
 
Does this sound like a plausible explanation? Is there anything else that I should look into that may have caused the previous low boost? There's no engine codes so it shouldn't be a knock / limp mode issue. I'm 92% sure that my guess is correct, but don't want to cause damage if there's another issue.   
 
Side note - very happy with the Blitz SBC. The graph display and record functions are awesome and it's super easy to setup and use. I was planning to get the OLED GReddy Prospec B but can't turn down a gumtree bargain. 

This stuff is unicorn blood. I don't know if the old oil was the wrong grade, or there wasn't enough of it, but my box is now smooth and crunch free.
 
 
 
I also found out over the weekend that my fuel cut still works. It kicked in at an indicated 13.3 psi.  
The rubber cap that I used to block the wastegate actuator to t-vsv blew out, and boost climbed from the set 10psi to fuel cut. I've fixed this with a beefier piece of capped silicone hose.
 
I was thinking abut disabling fuel cut and using the limiter in the boost controller as a safety net, but I've realised now how useful fuel cut is. The boost controller's limit and cut-off features only work if it's operating correctly in a closed system. If something fails - boost will continue to climb...
 
I'd like to run around 12psi (stock engine). Given how close that is to fuel cut I'll need a FCD to increase the limit slightly. Hopefully I won't hit cutout again but it will be good to know it's still there if needed.
 
Need to decide on HKS / twosrus/ or DIY FCD.

5SGTE
I stumbled upon my old hks fcd today actually. It's just chilling in the shed if you need it.

I'll PM, thanks  

Regarding the fuel vapour smells you really need to track that down.
Check that the various vapour hoses were correctly refitted to the funny looking vertical collector thingy behind the heat shields. Check the high pressure pipe union near the front engine mount and at the fuel filter.
Did you reseal all the gaskets that were disturbed along the top of the tank?

One more thing sorted out, from 5SGTE.
Further boost tuning on hold until I can identify the source of fuel smell.

jaycrab
The box has always been stiff and hard to select 1st and reverse, so fingers crossed the bushes gave out after a hard drive.
 
I'll try to pick up some skateboard bearings during the week and jack it up this weekend... 
 

Changing the shifter bushings is pretty easy, you can do it without even jacking the car up
Also, check under the actual shifter in the car. if a screw or something falls under the shift boot, it can lodge it will commonly vibrate under the shifter and not allow you to select any or certain gears. 

If you have always found it difficult to select gears, it could be the clutch master or slave seals deteriorate, or even the clutch hose can fail over time and swell up when you depress the clutch. 

Cheers, 

^ that would crunch though wouldn't it, if not disengaging properly? There's no noise or grinding, it just feels as though something is misaligned and preventing gear selection. The master and slave cylinders are both less than 1,000 kms old and bled recently. I'll take a look from the top when I can and report back.