My brain is now smoking... 
Slow down buddy
I did put in an extra ground from the head to the fender well a while back and it made no difference.
On the MAF, originally I had a Toyota one, then I replaced it with a remaned one and it ran better but still has issues. With the stick MAF it was beginning to dog out at like 2800 rpm, the remaned one I can get 3500+/- before it dogs out. My parts guy ordered me up another one to test and still no difference......
Ok, it's great you've got those grounds. Next, do you have the proper ECU for this engine? I mean the exact matching ECU that came with that harness and all equipment/sensors? When I was trouble shooting my lean-out issue when I had a TRD Supercharger installed onto my 1995 T100 3RZ-FE, I tried a 1995 Tacoma ECU and also a 1996 4Runner ECU and they ran HORRIBLY. The 4Runner ECU wouldn't even idle, yet they were all single coil 3RZ-FE ECUs. So I know there is a big difference if you start mix matching components across platforms.
Next, I would suggest the following: With the engine off, switch the key in the ON position and double check you've got the proper ground and proper Hot signal at every sensor related to the engine. I didn't wire the temp sensor in correctly on Bevin's quad coil 3RZ-FE initially and it kept throwing random codes and we couldn't figure it out (at the time I only had experience with single coil versions which have a separate temp sensor at the air box, rather than integrated with the MAF sensor). Then his Optima would drain completely dead within 3 days of not driving, and that is when I discovered that I had accidentally wired the power for his temp sensor over to a vacuum solenoid that would stay on 24/7. It never threw an error code for the missing temp sensor but once I got it connected properly it ran smoother.
Make sure you have the proper MAF sensor for your ECU. Early MAFs do not have an integrated temp sensor, later models do.
So I'd recommend something along the lines of remove the plug from the MAF and make sure it's ground and +Vdd signals are good, then reconnect the plug. Then do the same for your coil pack, and your igniter, and your TPS, and your ICV, and everything else. Cross reference them all with your Toyota wiring diagram and make sure that they are present where ever you should have +Vdd and -Vcc when the key is ON.
Took a drive just now with the scan tool. Long term fuel trim is like 15-17% at idle and from 25% to 37% while getting on it.
...
Is it possible with that cone I am just getting too much air for the ECU to compensate for?
...
I know the turbo/tuner set uses RX7 injectors that are a direct fit but like 440cc. Should I consider this route?
HOLY MOLY. Maybe the ECU doesn't like the signal coming from your MAF, because one of the other is not the right application or is bad. Sounds like so much fuel is being added that it hits fuel cut prematurely (your ~3500 rpm limit). Don't run any other injector but 3RZ-FE injectors original to your engine. Get it running properly first before you start monkeying around.
Maybe I have a nasty injector?
It's possible and this is very easy to check. Here is a picture of my Iridum plugs from my Supercharged MR2. I pulled them out last year before I smogged my car just to see how the condition of the engine was. In this picture they have about 45k miles and look to be in great shape:
All of your plugs
must have the same color to them. If you search Google Images for "spark plug color guide" you'll find a bunch of guides, such as...
or...
If you have one injector that leaks then you'll have 1 plug that is fouled out (much darker than the rest with a lot of carbon build-up), or if you have one injector that doesn't flow well then you'll have 1 plug that looks clean and the other three will be noticeably darker
Let's get this fixed one thing at a time
Regards,
BigMike
