Stepper chip has 2 power pins. You can put diode in series to prevent that(stepper power), or use p259, ign, inj.
all inj used, ign used, p259 too weak, 
used specfet now, but the correct way would be to rewire 4 ign outputs to stepper and use ign igbt's. so diode on power supply wire which goes to ec36-25 pin. why that is not default? any negative effects? what diode should I use?
What is exact purpose?
IMHO that is wrong way to make a wiring. Now you have energy flow thru protective diodes.
what do you mean wrong way? logic level ign over stepper ?
ign coils left on logic ignition channels, I use it for m54b30, 2 inj outputs vanos, 2 ign outputs idle, one stepper out safety relay, one shift light, and one I wanted to use for intake disa valve. p259 used for fuel and fan relays. if I put disa intake valve on stepper, I get that I turn on main power switch without ignition and fan starts working.. I have no idea what is wrong with that.. but on other output no problem totaly. it was the same with these few boards which had p259 protection diodes wired to ec36-25 pin when they were wired to flyback pin problem gone
