So this morning I swapped in my 460's. The only thing I changed was my required fuel setting. The car started fine, and I VE analyzed it one time, and everything looks good. I was reading the Megamanual and it says this:
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If you are running high-impedance injectors (greater than 10 Ohms), then set the:
PWM Time Threshold to 25.4 msec, and the
PWM Current Limit (%) to 100%.
(The presence or absence of the active flyback circuit (v3) or flyback board (v2.2) doesn't matter for high impedance injectors.)

If you have low impedance injectors (less than 4 Ohms), set the:

PWM Time Threshold to 1.0 msec, and
PWM Current Limit to 30% in most cases (all V3 main board with active flyback installed, and all V2.2 main board with flyback daughter board installed).
Set the initial PWM% to 75% if (and only if) you have low impedance injectors and have NOT installed:

the active flyback circuit on a V3 main board (assembly manual step #69), or
the 'Flyback Board' daughter card on a V2.2 main board).
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I'm pretty sure my RX-7 460's are low impedence, but according to my tune, it's set for high imp. What imp are the stock injectors? If I don't have my MS set correctly, why does it still run so well?

 

All the 460s I've ever seen were high impedance.

What's the denso number on the side of the injector. Cross refrence that to see what impedance they are. Or use a multimeter to check them. Maybe they are high impedance.

 

what's your point? you have high ohm injectors...so keep the settings the same...basically PWM is turned off.