Double check your Dawes/Needle setup against the schematic in my albums (link in signature). Nothing else that was done at that time will effect MAFv other than the EGR but not usually to that extent, idle voltage will go up from 1.7-1.8v to 2.1-2.2v because there is no EGR being blended just more straight fresh air being drawn past the MAF switch.
A 3" exhaust will raise spoolup but if it's been in 2 years there should be no change, how bad was the manifold leak and how long had it been there?
Can you manually hold 3rd gear and redo the spoolup rate test, that seems very low for a 3" system.
This really is right out of the norm and particularly with an auto as they are usually a little more forgiving. Spoolup like that is not high. Was the 3" on it or did you fit that? I will be very interested in what MAF v you have at idle and say 3grand.
It sounds like you have 2 different limp spots 2-2500 and then one just over 3000, assuming now that yours is a manual.
If you don't have an ECUTalk can you rig up a digital multimeter to the red wire of the MAF switch and give us some readings at idle and with a few revs on board?
You may need to consider adjusting the VNT grub screw down a bit (1/3-1/2 turn) or fit a JayCar MAF voltage modifier. But this degree of obstinacy is not the norm for a relatively minor modified vehicle.
We haven't been through the spoolup rate exercise yet, what boost do you have at 1500 and 2000 under heavy acceleration in 4th gear? What year model is yours again?
OK we are getting somewhere. It will be magic MAF voltage for sure and that won't trigger a MIL lamp. I would be reconnecting the Dawes and needle, making sure it is as the schematic bypassing the vacuum switch, either Chaz's or mine, and then just keep slowly opening the needle valve until the limp stops, then we will have some idea.
Can you equate a rpm to the limp, near as you can get it.
If nothing else works (and sometimes it doesn't) there are devices like the JayCar voltage interceptor and the TurboSmart FCD2 to defeat it.
I also have a thread in the build section Geeyoutoo, the Troll, which covers many of the mods and adjustments as well, also in my signature there is a link to my albums which does have some detail on MAF voltages in the JayCar install.
The Dawes is quite easy to install but not so easy to setup if you have a drama, it takes a bit of time to get it right and experiment with needle valve settings, you may need the needle valve open up to 1.5 turns to get the result you require, also there is the possibility of a small VNT adjustment to assist as well. The vehicle will go much better with a Dawes than without, once you get it right, do you have it setup according to my schematic?
Have you read the articles in the DI archives, specifically the NADS, so you bought a ZD30, which is the very first thread in the first post? this explains a lot of what goes on.
As for getting rid of limp electronically there are a couple of ways, the TurboSmart FCD2 will get rid of one limp area and I had one fitted for some time and then a secondary limp came in from other mods and it could not cope with it, so I built a JayCar Voltage Interceptor and have control of both now. There is a very long current thread on this in the DI section.
(post too long have to do it in 2 sections)
This needs some qualification as it all depends on what mods you have, blocked EGR, big exhaust, big IC all add to the mix, but put simply, yes, if you have spoolup high then you could theoretically hit around 4v under 3000rpm (3.98v is the magic number in mine) and the ECU doesn't like that. By slowing the spoolup you reduce the speed the MAF voltage climbs and get rid of limp.
But as said it all comes down to what you have, for me to get rid of my limp completely I would need to have the spoolup rate that low that it would have effected performance, hence the electronic way we do it.