Hi Chris,
This all sounds very familiar. Lets see if I can add some value...
>What I mean is it is starting within a couple of blades
That's better than mine now. I start after 2 or 3 revolutions of the prop.

>I am getting the volt reading on the EM2 flashing most of the time.
What voltage reading is it flashing at? You can adjust that it its too high.

> when I shut the primaries down at a higher RPM the engine stayed running on the secondary's
Thats part of my run-up check. (along with shutting off one set of coils, flipping fuel pumps and flipping to B computer)
Shutting down the primaries does cause a noticeable hesitation. It sounds like its going to doe, then picks up again.

>I have been able to get idle as low as about 1200 rpm, even though it is pretty rough.
Mine idles smoothly at around 8 - 900. With the IVO on full fine 1200 will be "fine" on approach. With the big fixed pitch prop 1200 would make the plane much less inclined to stop flying, but with the IVO chopping the throttle makes it sink  quiet nicely. (Add both rudders and you're in an elevator). Watch out for the difference if you train on a fixed pitch - this caught me by surprise the first few times.

I saw a comment about gear chatter at lower RPM - I've heard one or twice in the past, but do not get it at all now.

>and then came out of auto tune mode.
Remember that there are two sets of tuning numbers, one of which controls mixture when the engine is being driven by the prop. As far as I remember, the second set cant be tuned on the ground. This caught me out when I throttled back on the downwind and the noise went away. A rapid manual increase in mixture brought it back, but it had me going there for a while.

>I got to about 5500 rpm and my RPM reading on the EM2 went blank.
Could be a vibration / connection issue.

>my temps are not all that bad considering the high heat on a stationary bird...
Not bad at all. In those conditions (S. Florida) my temps stabilize  at around 210 so long as I don't give her much over idle. As soon as I do I'd better be ready to roll because it'll get over 220 fast. By the 5500 WOT on the IVO sounds good - if its the 3 blade 68 like mine - thats about what I get.

Regards,
John