The circuit now looks good. However, I have not checked it thoroughly, just a casual glance over. By isolating the 2 grounds and the 2 supplies, what you have done is eliminate the electrical intermingling of currents. The radiation aspect is what you now need to control. For that, everything you read in the rule book for HF design and high current design should apply.
I am willing to wager on you solving your problem by just separating out the 2 supplies and grounds like you have in the new schematic.
You need to ensure that the PIC does not brown out during the time one/maybe more MOSFETS are on and the engine is revving. This is the time you will see brownouts if your 5V power is not well regulated. Like I said earlier, a simple 1N4007 diode followed by a reservoir capacitor feeding your 5V regulator should keep the PIC happy. The best way to check would be to ensure that the circuit stays on for at least half a second when you remove power. Now, come whatever spikes due to the engine rev, you will still have the PIC running safely.
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