Consider changing the O2 sensors if you haven't done so. A vacuum leak can also cause issues as air gets past the MAF and the fuel trims are bumped up. You can also burn off any impurities in the cat by going WOT for a period of time or by using Seafoam.
I have the smog reports of my 1MZ MR2 which is setup just like the M/T 1MZ. It didn't fare well the first 3 times at the BAR. I'm running a CA spec ECU though which isn't proper for this setup.
HCs are unburnt fuel.
Feel free to look at my smog reports:
https://picasaweb.google.com/jasonmzw20/SmogReports1MZ#
For the passing report I resorted to using a one step hotter spark plug. It has a new cat, cleaned/balanced CA spec injectors (10cc larger than M/T injectors, not good for smog either), new AFR sensors/post-cat O2 sensor, etc.
If your CO2 is 14.8-15.2% and O2 is less than 0.2%, the combustion within the engine is efficient.