I'm not an expert on this machine, but a couple of things kept bothering me as I read through this (multiple times!)
The Cylinder head:
Did you ever get an accurate gauge on bolt torque? 14 ft/lbs doesn't sound unreasonable for a little engine.
You mention the compression is much higher than spec. Do you think you're getting detonation?
Since you removed the head, you know there's no carbon buildup. but what about valve train? Could the timing of valve train be off causing the high compression? (assuming the valves are adjusted correctly).
Ignition:
My first thought was coil and/or wires also but it seems you've replaced spark plugs/coil etc. to no avail - is that right?
Does that engine use "wasted spark"? I couldn't figure that out from this thread? Could the wasted spark be causing detonation or similar if the valve train timing were off?
Is the spark system getting enough power? Have you tried a new(er) battery? Are all grounds clean and good? Battery terminals clean?
Fuel:
I think you say the engine is always running rich which is showing as blackness on the spark plugs.
Since this thing has a computer controlling it, what would make the computer think the engine was too lean? Temp sensor would do it - possibly stuck thermostat?
Is the gas in the tank old/have water in it?
I hope this helps and I hope you get this figured out.
Thanks for taking an interest. I'll try to answer all the great questions below, in the order you asked.
1. I did get the head torqued to factory specs finally. I had to replace all of the head bolts with new and had to buy another new head gasket to get this correctly repaired.
2. Using a standard compression tester, I'm getting 200# from each cylinder. The shop manual specs 185#. I don't think I'm getting any detonation though. Just an annoying misfire.
3. I'm fairly certain the valve timing is ok. I've adjusted the lash twice now and verified the timing marks on the crank and cam. I do plan to check the lash adjustment one more time though because I've learned of a different method which seems (I think) to be better. None the less, it's making 200# compression so I'm thinking it's probably not totally out in left field. Unless the lash setting is somehow causing the high compression as you mentioned, which I'm struggling to understand how that could happen, but I'll admit it may be possible.
4. I have replaced the spark plugs, injector, ecu, coil & wires and MAP sensor. I do think it has to be a wasted spark ignition because it's a single coil with 2 plug wires. I guess it would cause poor running conditions if the valve timing were off. It doesn't run horrible, just doesn't run great. Also, it has improved vastly with the replacement of the ecu and MAP sensor. The ecu, MAP and coil replacements were used from ebay.
5. I'm getting 12+ VDC from the battery standing and 13+ VDC running. I pulled and cleaned all of the ground wires/lugs and battery terminals. Great question here. I admit though, I have not tried a new battery, only because I can't identify a problem with the current one.
6. I did verify the fuel pump pressure is above 36# per the shop manual. I deleted the charcoal canister and removed the tank, removed the pump and cleaned both refilling with fresh ethanol free gasoline.
I also hooked up my timing light to see what the spark timing looked like, which looked very erratic. It wasn't what I was expecting. Basically, I'm down to thinking that there may be a problem with the crank trigger or flywheel. Problem is, I believe the entire rear carriage has to be removed from the buggy and then the engine has to be separated from the transaxle just to gain access to those components. I'm pretty much waiting for the fall to attempt that project. I really like to avoid it all together by just abandoning the factory engine management system. The one caveat with that plan is if there is a problem with the flywheel key, I still need to address it regardless so...I don't think I can avoid tearing it all apart. I think what will likely happen is I'll break it down to get all the modifications necessary for the aftermarket ECM done, and I'll check the flywheel while I'm in there. Its really tedious and annoying trying to troubleshoot this problem with no access to the ECU so given the choice, Ill abandon the OEM computer without much concern at this point. It's been a really odd experience trying to get information about repairing this apparent unicorn side by side. Doing the usual YT and internet searches come back with practically nothing. That never happens. But the older RTV-500 seems to be the exception. I still think it's a cool little machine but now it's simply a battle of will. Challenge accepted!
Thanks again for taking an interest. Let me know if you can think of anything I'm overlooking. Best wishes.