912is won't run with "start power" off

If it starts and runs, the lanes are powered and wired correctly.
The Fuel Pumps are good and the ECU is operating.

Once the engine starts, the Fuse Box will internally disconnect the Start Power and operate momentarily on the B Generator.
After a short period, it will internally switch to the A generator if available.
What you have is a Double Generator Failure.
This should be your point of interest.

Assuming both the Grey and Black Gen Plugs are connected and the internal Gen fuses in the Fuse Box (The BIG ones) are good ...
Did you connect the Gound Wires from the harness to the A and B regulator correctly?
There should be 3 Total on the B-side and 12 total on the A-side.

When you switch either Start Power or Backup Power you are also switching the GROUND connection from the ECU Bus to the Battery bus.
Check that you are disconnecting the proper circuit connections.

"Did you connect the Gound Wires from the harness to the A and B regulator correctly? There should be 3 Total on the B-side and 12 total on the A-side."

This appears to be the problem, but it's confusing. I bought this engine used, it's got about 500 hours on it. All the grounds except the airframe ground were already landed on the fuse box. But it appears that the 12 wires are landed on the B side. Either that or I'm mistaken on which is the B side. 

The manual shows the B side being on the right when the connectors are pointed down. That would put the B side on the left with the connectors pointed up as they are in my installation. It also shows the B side has a grey connector, A side has a black connector. My grey connector is on the left. The 12 wires are on the left which I think is the B side. Bill's comment says the 12 wires should be on the A side. 

You can see in the picture where I put the yellow label on the fuse box that says "rectifier B", but there is a wire going to it that says "regulator A". I guess I never noticed the mismatch. 

The 12 wires don't appear to be long enough to reach the other side of the fuse box and land on the other rectifier. I don't understand how they could be on the wrong side, they only reach one side. 

Hopefully, this would be as easy as moving the airframe ground to the other side. But that does not make sense as the looks like it should be the A side. 

Thanks in advance for any help.

Jack

Yep!  The grounds are on the wrong (B) side.
The A-side is on Your Right (Connections UP) with the BLACK Regulator Connector as you correctly have identified.

With START or BACKUP Power applied the Grounds are cross-connected.  Game On!
When you release START Power, you are also removing the grounds.  Game Over!

The harness is plenty long enough.
You may need to remove some cable ties and re-route the harness but they will easily reach the A-side.

BOTH Sides should have an Airframe Ground (Heavy) cable.
The B-Side cable should be permanently attached to the Airframe/Battery Ground.
The A-Side cable will pass through a START Switch/Relay before also connecting to Airframe ground.
The A-Side Cable is connected to the Airframe/Battery ONLY when START or BACKUP Power is enabled.
- - -

A-Side = Nine (9) Harness Grounds, One (1) Fuse Box Ground, One (1) Regulator Ground and, One (1) Heavy (12AWG?) Switched Airframe Ground.   Twelve (12) Total.

B-Side =  Two (2) Fuse Box Grounds and One (1) Heavy (12AWG?) Un-Switched Airframe Ground.   Three (3) Total.

- - -

If the previous owner did NOT disconnect the START Power Ground during normal operation, it would have worked.
There are a lot of improper installations flying around out there!

Bill 

Thanks for the prompt reply and all the help. Makes perfect sense now that you explain what going on. 

I can't quite wrap my head around how it got wired backward. I bought the engine used, it came out of a CT cruiser that was involved in a landing mishap. It appears to have been wired that way in the CT Cruiser which is a certified LSA. Must have been done at the factory. I can see where having it wired like this would make the engine considerably less reliable. 

I'll get the wires swapped around, but it sure looks like this is the problem. I'll report back and let you know if it's all working correctly. 

Jack

I got the fusebox rewired so that 9 wiring harness ring terminals are landed on the A-side of the fuse box where they belong. Everything works properly now. Engine runs with "Start Power" turned off as it should. 

Along the way, I traded contact information with Bill H and had a couple of conversations with him. He is very knowledgeable and I'd like to thank him for his expertise and time in helping me figure this out. I thought that I'd bought the engine with the ring terminals on the B-side, but after talking to Bill it's obvious that I put them there myself. Don't know how I managed to do that, it's clear in the manual where they go. 

One thing I've never understood though this entire installation is why have a "start power" switch at all. What is the point? There is no explanation in the manual. I thought that it was to somehow make the engine more reliable. Make it so that a short or something like that in the airframe would have no effect on the engine. After talking to Bill, I became convinced that connecting the engine harness ground to the airframe ground would have no effect, so that's not the explanation. Bill's theory and I think it's just a theory, is that it's wired this way so that the fuel pumps will shut down if and when the engine shuts down. With the A-side disconnected from ground, the fuel pumps can only receive current from the alternators. If the alternators quit working the pumps don't get any electricity and shut off. This could be important in a crash so that pumps don't continue gasoline and fueling a potential fire. 

That is in fact how it works. With the lanes and pumps turned on and the engine running, if you turn off the lanes the engine quits and the pumps stop even though the switches for the pump remain on. 

Cars have an inertia switch that shuts down the fuel pump in the event of a crash. Rotax gets to the same place by running the pumps only from alternator output, no output the pumps stop. The "emergency power" switch keeps the engine running from the battery in the event of alternator failure. 

I learned a lot and again, thank you Bill for your help. 

Jack