I don't have the exact procedures (can't remember it on top of my head), but you'll need a Toyota "SST" timing gun for checking timing with the 1MZ's individual coil packs. I have a custom "jig" to set up my timing gun so it could pick up a signal after the coil packs when I check my timing (only because I am running a standalone ECU that I need to sync the base timing)
Base timing shouldn't be affected at all under any circumstances except for a malfunctioning crank angle sensor or ECU. You don't need to "adjust" anything for the 1MZ
If you are sensing that the engine is over retarded, it could be your knock sensors pulling the timing. Maybe put in higher grade fuel and see if the problem still exists. Or else, you'd probably have knock sensors that are getting too sensitive just from old age or wear and tear (common problem for the Gen3's). With retarded timing, the engine can't burn out all the fuel properly which causes a rich condition. Try to fix the timing/knock sensor problem first before deciding on getting an SAFC to lean out the engine.