Brands of ECU's or FI/C that allow OBDII to work
 

I'm thinking I'm going to have to switch to a different ECU or a piggy-back FI/C so that my 2000 SE will be OBDII compliant. I live in a Chicago suburb that receives the invitation to come in and be plugged in.
Current set up is:
Mega Squirt DITPNP MS2Extra 3.0.3s
FMII GT2560 turbo kit
MAP, 550 injectors, COP, cat delete.
Besides putting it all back to stock, (which isn't really an option) what have other people done to pass OBDII? I was looking at AEM, they have a piggy-back Fuel Injection Controller (FI/C) that I'm told works with the stock ECU. I'm told by AEM and a couple of their recommended tuners that this is a workable solution. I just want to see if there is something better out there that I should look into.
Thanks for the help,
-JB

Given that you seem to be running fairly large injectors and a reasonably power-capable system, I'd strongly advise against abandoning the MS altogether and diving straight into a piggyback system, especially one which limits you to AFM adjustment as a means of injector control.

Have you considered performing a parallel install? You could utilize your existing DIYPnP (by opening it up and bypassing the ECU daughterboard), and use a Boomslang ECU Extension harness to intercept the factory harness.

Last time I did emissions I ran the car on the stock ECU and injectors just long enough to get it to set the I/M monitors. Do you still have most of the stock wiring in the car? I could help you try and set it up in a way that might get the car to pass.

This year I just changed the registration on my car to my sisters address in Rockford to avoid it.

Joe, thats a good suggestion, but I have to admit I'm "electronically challenged" when it comes to going in and changing stuff in the ECU. It sounds like the AEM won't be able to supply my fueling needs. Could you please explain.
Aricjm15, sorry, I don't know what the I/M monitors are. This sounds like a possible solution. It's a MS plug-n-play. I didn't think the car would even run if I plugged in the stock ECU.
The good news is I haven't got the invitation from emissions yet (maybe a year away, maybe)
I would eventually like to set the car up for E85. So, the least expensive solution would be preferred, as long as it works like it's suppose to.
-JB

Its a checklist the factory ECU has to go through to tell that everything is working OK. Since your car is a 2000, you are aloud to have two monitors not set. The only one that needs to be set as OK is the catalyst monitor. Even if you don't have a cat it is easy enough to fool the factory computer.
You will be able to "drive" the car, on the factory computer, but something will need to be done to keep the engine from getting any positive pressure from the turbo.