MicroSquirt.com read only forum (Jan.15,2018)

This link should help you check what size your injectors are.
http://thegebharts.com/msindex.html
I think you will find that if they are 45lbs they will be too small for that 360 at higher RPMs and load, but you should not have any problem at idle. Sounds like you have some other problem.

What is your MAP source? What does it read with a vacuum gauge? The first thing I would check is if your MAP is reading correctly compaired to engine vacuum. 80 KPA is only aroung 6 inch lbs of vacuum. Is that what you are running?

I have been running a Pertronix unit in the stock distributor my 69 Mustang 351W for some time now. It is working great.

:RTFM:
http://www.megamanual.com/ms2/pcb.htm

"PWM Flyback On-Board: The flyback and synchronous rectifier (flyback damper) circuits are now on the V3 board, so no external flyback board is required as was the case with version V2.2 MegaSquirt. This is a build option, so if you are using high ...

The flyback board is definitely the best way to go.
But if you want to use resistors, they will work, but you may need to experiment.
You are correct on the total ohms. Just add the injector and resistor.
I would start with 1.5 amps hold current. The spec's I saw for your injectors show them at 2.9 ...

Have you read the injector section of manual?
http://www.megamanual.com/v22manual/minj.htm

"....To eliminate PWM altogether, use a 5 to 8 ohm resistor (with a 20 to 25 watt rating) in series with each injector. "

I did some research for you.
You can find a service manual here
http://www.zeroyon.com/index/content/view/24/47

Look in E_Theory.pfd

The AAC valve appears to be a PWM closed loop used for 'fine tuning' idle speed.
The 'Air Regulator' is a warm-up valve, the wire feeds an electric heater to help ...

Could you use the AAC solenoid for warm-up, controled by MS "Fidle" output, use the idle screw to set your normal idle speed and then wire the FICD to the AC compressor (with a relay if needed) to turn on when the A/C kicks on?

Yes,
You treat low impedance injectors with resistors in series (NOT Parallel) the same as high impedance injectors.
Below is a cut from the manual at http://www.megamanual.com/v22manual/minj.htm#injresist

--------------------------------
Injector Resistors

However, instead of the flyback board ...

BlackHat
As James said above, speed density method allows you to increase idle speed simply by letting more air into the engine. This can be done by an air valve of some kind, by cracking the throttle, or even a vacuum leak. When the MAP sensor sees more air (less vacuum), MS squirts more fuel and ...