I've had to deal with the Indiana emissions test in Lake County twice. I passed with flying colors both times, even though my car was modified. For those who don't know, this is a test only done in a few counties in Indiana (Lake and Porter up by Chicago, maybe others). For our GN's, they put the rear tires on rolls, insert a sniffer into the exhaust, and drive the car at a certain speed (I think it was 25 mph). It's a simple test, but difficult to pass if you don't have the right stuff on the car.
Here is what I did to pass the test:
0. HC or CO can be caused by misfire. Make sure your spark plugs are good, wires are good, coils are good, etc. If the car is noticeably misfiring out the exhaust at about 25 mph, you will likely fail. Also, make sure your O2 sensor is in good shape - make sure you see lots of cross-counts on the scan master while you are driving.
1. In my case, I installed a brand-new catalytic converter. Having a new catalytic converter is 90% of the battle. The converter needs to be nice and hot when you take the test to ensure it's working efficiently, so go drive the car on the highway for a while before you take the test. Having the car hot will also help the O2 sensor be more active (especially if you are still using the stock non-heated sensor). In my case, I may have taken the converter off after the test and replaced it with a test pipe, but I can't remember for sure

I went so far as to rev the engine while waiting in line to keep everything as hot as possible.
2. Re-enable the EGR system - This is usually needed to pass NOx. I burned a chip myself that would run the EGR valve in a stock way. If you are not failing for NOx, you might be able to get away with leaving yours blocked. Having the EGR blocked should actually help you with regards to CO2 and HC - surprised you failed on those and passed on NOx.
3. Disabled my MAF translator and installed a known good stock MAF. Sounds like you already did this.
4. I ran the test with about 2 gallons of E85 mixed with about 10 gallons of 93 octane. The E85 will help with CO and HC.
5. Are you still running a stock chip? If "yes", then doing the above should get you through the test. If you have a more modern chip, then set it up to do the following:
a. Change the fan turn-on temperature to be much higher, like 195 degrees. If you can't change this in your chip, then consider either unplugging the low-speed fan relay or controlling the fan manually. The hotter you can get the car, the less HC and CO it will produce. However, it may produce more NOx, so don't go overboard.
b. Make sure the chip is running the car in CLOSED LOOP at idle and under load. If it's running open loop, you are pretty much guaranteed to fail for HC or CO. That catalytic converter won't clean up much if the mixture isn't constantly changing from rich to lean under the command of closed-loop.
Hope this gets your through...
Mike