So to start, I am building a transmission control module to add paddle shifters to my Jeep. I got everything built up and put together so when you hit the + paddle it upshifts one gear and - downshifts one gear. There are only ever 2 relays energized at the same time. 2 for the main gear solenoids in the transmission and 1 for the torque converter lock. The code is set up for 1st gear to energize solenoid 1, 2nd gear energizes solenoid 1+2, 3rd energizes solenoid 2, 4th gear is all off, and 5th gear is solenoid 3. There are two 5v, 1.5A voltage regulators, one for the relay boards and one for the Arduino Nano. The Arduino and relay boards share a common ground and the voltage regulators share 12Vin off of the factory transmission computer harness. I am using 2 of those cheap chinese 2 relay modules with optocouplers and flyback diodes installed already, the jumpers are removed and I have the arduino connected to Vcc and the INpin, the voltage regulator is connected to JD-VCC and ground. So my problem here is that everything works fine with the transmission solenoid 12v load disconnected from the relays, but when it is connected, the relays sometimes will shift erratically when you try to change gears. Its never the same way each time, sometimes if you shift up a gear it will bounce back down so you have to click the shifter again. Sometimes if you shift down a gear it will shift back up. Sometimes it will skip over a gear. I have browsed forums with similar problems to no avail because none of them really share my exact problem. some people say you need a capacitor across the input switch, some say you need a mosfet (I don't know how I would be able to use a mosfet to switch the high side of the circuit), some say you need a SSR. Some say you need a better power supply for the relay module or you need to use 2 separate power supplies (I tried powering the arduino off a usb charger separate from the relay module and that didn't work. I couldn't do that permanently anyways because I only have one source of power from the vehicle). Is there anything obvious I am missing?
Your problem are the solenoids which cause heavy EMF when turned off. Put freewheel diodes over the relay contacts which support the current drawn by the solenoids.
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Diodes should be across the solenoids, not the relay contacts, post a wiring diagram.
Bit tricky with that word salad! 
We need a proper schematic to untangle it. 
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