912 ULS with 460 hours built in 2008 1000 RPM drop during Mag test

Interesting, the when the engine jumps to a faster, smoother state it happens at differing times.  Originally, I was impressed on how crisp the engine started.  Every time. Through all of my engine test time in the garage, to the first 5 or so hours of flight, the engine started right up.  Now that first start of the day takes a bit to get it going.  Then at an ok, semi rough idle it just snaps into a faster smoother engine.  It can be 3 seconds, it could be 10 seconds, but it always happens.  To start it now I try the choke at first where it sputters a bit.  Then I try just a bit throttle and it will start.  Sometimes I have to repeat the tease with the choke and then try the throttle again.  Never at the same time though.  It did not do this in the beginning.  Its electrical and I don't what it is.   I do have a big capacitor between one of the regulator connectors and ground.  Should I disconnect that and try running without the capacitor?  I really don't think that is it being that the engine was great in the beginning.  The wiring hasn't changed, so what is happening here?

The Capacitor is there to give the Gen a Load when the Panel might be turned OFF.
That is Not the problem.

The RPM Changes are interesting.
I have a 912is engine, so little soft start experience.  However, if I recall ...

A soft start engine starts smooth and fast, and a few seconds later suddenly slows down and power-rumbles a little as the spark advances to the BTDC timing.
The Opposite of what you are seeing.  Someone else please comment on this.

What are the Part numbers of each of your Ignition Modules?
Some Soft Start Modules do not have wires, they just time out after the start.
Only one may be a Soft Start version, and it may be STUCK in Soft Start mode.
You might not be looking at a 1000 rpm drop as much as a return to normal by removing the 1000 rpm increase when you kill the fast Mag.

I don't think that I have a soft start system.

When I do a mag check on the problem switch the engine almost dies.  It keeps running, but in a very diminished fashion.

OK, I concede on the Soft-Start Option.
For Future reference, Apparently, Soft Start Modules have YELLOW Serial Labels.

We need to isolate the problem.
I know you have done this before, but let's retrace our steps.  2 steps back, 1 step forward.
Let's swap BOTH sets of connectors on BOTH Modules.
If you have to remount the Upper and Lower Modules to perform the swap; so much the better.
Often getting deep into the hardware reveals the problem.

If the problem remains on the same side, swap the Spark-Coil Connectors back to the original modules.

Something needs to change!

Ok, yet another test today.  
I swapped the 6-pin input plugs leading to the CDI boxes AND the output plugs going to the coils.

NO change was noticed.  I kinda expected that being that I swapped the input plugs several times already.  Being that the problem stays on the same switch tells me that the problem is not from any component from the plug on down.

I did though discover something in the Heavy Maint manual about one of my other problems where the engine suddenly bumps itself from a ok power setting to a stronger rpm just like a switch had been thrown.  I said before that I have noticed this behavior anywhere between 0 and 10 seconds.  According to the attached manual diagram you can see that there is a full ignition mapping delay of ANYWHERE between 3 and 8 seconds.  That explains that problem so its not a problem.  I also noticed that this is only on first start up or if you let the engine sit a bit.  Otherwise the engine starts right up.  Why random between 3 and 8 seconds?  I have no idea.

I STILL have the "mag" check problem and the hot 3 and 4 EGT problem to find.  So frustrating.  Weeks of flying wasted.