Mrskylighter

Have you reset the ecu after making these changes/repairs?

Sure have. I have been taking out the fuse to reset the storage of error codes. Not that it makes a difference as every time i check for error codes after the engine malfunction light comes on it says there is nothing wrong with it.

I assume you have a gen3 NA engine service manual?
There is a free download in the tech section of the forum. It has test procedures for the VSV

Yeah sure do. Hopefully i will have some time to test it later tonight.
 
Toyota has quoted $144 and 10-15 days from Japan. Would you or anyone else happen to know if there are aftermarket solutions for this? I have done a quick google search that unfortunately returned nothing. 

Update:
 
Since my last post i have checked the VSV and it was well with in BGB specs.
 
I have also given up on playing garage mechanic and have left the car in the hands of MRC Castle Hill who have not found the root of the issue but have found after dyno-ing and testing that the car is running very nicely and power is as per stock spec however the irregular running is due to the fact that the computer has advanced the timing by 20deg. What they cant understand is what is causing it and why the engine isnt pinging due to the large increase in timing and is running relatively good.
 
Time will tell. 

Mark and the boys at MRC will find the problem. I can't praise those guys enough.  I'm taking my car there shortly to do a major service with some other additions.
 
Are there any updates?

Mark did a great job in trying to find the issue. It was nice dealing with someone that has knowledge and experience with these cars. Although in the end Mark didnt find any issues like the ones i had been experiencing, though what he did find was that when he put the car in diagnostic mode it wasnt locking the timing, so there is a possible ECU problem there. He also reset the TPS after finding that the TPS error code came up every now and again. They continued doing many dyno runs without finding any issues. 
 
Iv had the car back since last friday and it has been driving with no issues as of yet. My theory is that it was a really bad batch of fuel or that whatever the problem was is severely intermittent. 
 
 

It must have been a REALLY bad batch of fuel. Haha. Good to hear that everything is back on track and you're back on the road.