As long as you're running the stock ECU, you're going to be running stupid rich, and very conservative timing.. Toyota is known for doing such, especially on their turbo'd vehicles.
The problem with piggy-back units is again, the stock ECU. They'll hold a tune for maybe 500 miles and then it will re-learn the specifications and override the piggy-back, another common issue with Toyotas.
I strongly suggest not opening the AFM. This is an oldschool trick people did back in the day to richen and lean out a fuel mixture, however it has been concluded it's more harmful than anything in the long run. I did extensive research on this myself, when I was tinkering with my old 16v 4AG.
You would really be best off with a standalone if you're really looking for the best numbers, even if it's not in your price range.