Only running on Cylinders 3 and 4 how is this even possible

How do you know that it is only running on specific cylinders, EGT?

The way that the ignitions are configured means that if one dies the other one should spark a plug in each cylinder. You could use some series spark testers to see if you actually have sparks occuring during the fault condition.

It is more likely that there is a fuel related problem. I would inspect the carbs and look for debris in the float valve and jets.

I agree that from what you have described it is somewhat perplexing.

I checked the jets. They are clean and installed per page 73-00-00 page 25 in the manual. 

As I research i suspect trigger coils could cause this. 

I did have to pull them to get the ring mount on...

However, I would think it would have run poorly from the beginning if that were.the case? 

Because it ran fine then started to misbehave it makes me think I may have lost a ground somewhere, but I just don't understand where I should look. 

Oh and yes, EGT and the old fashioned hand on headpipe test is how I determined which cyls were running a d which not. 

Let's confirm we are looking at the same modules.

You have two ignition modules.
EACH module has a 4 pin connector, a Ground Wire and 6 Single-pin connectors.
The 6 connectors at the module are White, Yellow, Orange, Brown and Two Blues.
Plus the Black Ground Wire.
Do we agree ???
- - -

The Black Ground wire should be Grounded.
The Brown Wire should NOT be Grounded. (Mag Switch)
- - -

Either module is capable of igniting all 4 cylinders on its own
You have two problems, Probably related.
When you see the problem again, run a Mag check.
I am guessing One Mag will have NO effect and the other will kill the engine.
On second thought, Run a Mag check.

Closely inspect your 4-Pin Connectors.

Well yes and no. 

I have the old style modules that look like this (attached). You are correct about the ignition switch, when this happened one switch had no effect. 

Also by the way I have mine set up with two switches for each module to ground out the engine and a push button start, I had it this way in the old plane too and prefer it.  

The ignition module you picture is shown in the Heavy Maintenance Manual Sec. 74-00-00 Pg. 31, Fig. 74-21.

If swapping the White and Yellow Single Pin. Connectors also swapped the working Cylinders from 3/4 to 1/2; This indicates that the module is Bad/Intermittent OR the 4 pin connector is losing the 1/2 trigger coil.
Measure from pin 1 to 2 and from pin 3 to 4 on the 4 pin connector.  Both readings should be similar.

The Mag switch test shows that the Lower Module is NOT Working at all. (BRN Ign. Wire Grounded ???)

Swap the Modules completely. Upper to Lower.
If the problem moves you have a bad module.
If it stays the same, you have a wiring harness problem.