EDIT SOLUTION AND LESSON LEARNED!!!
First the lesson, if you have double checked things, triple check them, if you have triple checked, quadruple check, then quintuple check, keep going until you have success. Check all of the basics every time you make a change.

So we don't understand exactly how, but the trigger wheel is backwards. I will flip it tomorrow to confirm but it is backwards on the car now. Tracing steps backwards we can deduce that 2 of us separately put it on backwards when we thought we had it right, we knew and both understood the proper orientation. One of the first things I tried was flipping the wheel. The biggest thing we don't understand is why we did not find it when we flipped it. The only logical conclusion we can think of is during some of the tests something else may have been wrong and we did not identify the wheel as being correctly oriented. During the final install I broke a bolt off into the center piece the pulley attaches too. I must have gotten it flipped around when I corrected the problem by replacing the center piece with a spare. Old man eyes may be a contributing factor during that final install.

I want to thank each and every person both here and on Facebook that helped out. If I told you that you were wrong about the wheel being backwards, well I was totally wrong, and I eat my words. Log off feeling proud, you deserve it. Mostly, thank you to the guy that urged me to look one more time, just in case. You know who you are. I'm just glad I can move on with the build now.

Original Post:
Alright, I'm at the end of what I know to do here. I've asked a lot of people. I've been to the MS Miata tuning group on facebook and stumped everyone there, they pointed me here.

I have a base timing issue, We have explored every last one of the common causes. This is the 5th motor that has been in this car. I will list some of the things we've tried below.

My car is a 2000 running ms3. My built motor is being worked on so as a backup I just swapped in a motor from another car (totally stock, ran perfect) after doing oil pump, water pump, seals etc... put a gates blue belt on it. I cannot for the life of me get this motor to set base timing correctly. With the offset to 20 (the max) the timing marks are at the top of the pulley. About 30-40 degrees. With the offset at 10 it runs like crap. With the offset 0 it won't run.

I believe the timing is being reported correctly, the motor sounds like it is running very advanced. As you increase the offset it runs like crap until it dies.

I do not believe it is the timing belt position. We've had a ton of people look at it. The timing variance is something like 50-60 degrees (30-40 that is reads + the 20 offset). A tooth, a few teeth even on the crank will not account for it being off that far. The cams are fine, they are not different, they are stock undamaged and both have the positioning pin.

I'm going to try to include some pictures and a video and some pictures. The video makes the marks look less stable than they are. The video does not capture it well with the timing light. It is clear and stable when looking at it in person.

I've checked every common item, here are some listed below:

• the car is an NB, there is no adjustable CAS, it has a cam position sensor
• the tune in the car was used with a different motor a week ago, that motor ran and timed fine, nothing has changed in the car other than the motor swap
• timing is set to fixed at 10 degrees, tunerstudio gauge reports 10 degrees
• lower offset moves the marks counter clockwise, raising it makes the marks move clockwise but it maxes out at 20 with the timing light reading 30ish, maybe a bit more. Offset needs to be at 15 to get it to start and idle reliably. Setting offset lower makes it run worse until it doesn't run. Last motor I had in it needed an offset of 7.1.
• retimed/checked the belt 3 times (see pictures taken with the motor untouched between photos)
• dampener properly points to TDC, I tried another dampener to see if it looked like it had slipped, tested TDC vs both dampeners with a screw driver, they both line up perfectly
• 2 different trigger wheels, it is properly oriented with the bulge to the front, I even tried it backwards, it makes it worse, but it still starts - this is where we screwed up
• more than one cam position sensor, more than one crank position sensor
• using dumb timing gun, bought a new one, it reads the same
• with the supercharger on or off
• the reading on plug 1 and 4 are the same, 2 and 3 read at the 6 o'clock position
• I put stock coils back on, same thing
• The car has full RPM sync
  

See pictures showing current belt position and video (with cussing) showing where the marks are at.

What have I done wrong?

(don't mind the supercharger belt trying to come off, I am aware)

 

Can you post a screenshot of your ignition settings? Also I assume both the trigger wheels you used were stock type?

I know you probably checked this, but were the cam gears installed with the correct dowel pin position? The more I check through your list this seems like the only unaddressed mechanical thing I can think of. And considering the tune was working on another engine I would start with either mechanical or sensor issues.

 

Have confirmed that the balancer timing mark is in the correct position? If you are using a fm trigger I believe they can be installed backwards or flipped.

 

That was addressed in his post

 

I should have read the fine print better, ha. This is a head scratcher.

 

Here are some additional shots showing ignition settings as asked. Plus additional shots of the motor aligned at TDC measured with my measuring rod with a rubber tip.

 

This is my settings with a 36-2 trigger.

 

Wait wait, so the bump "bulge" on the wheel is going towards the radiator (picture 2 in link), or the center section is going towards the radiator (picture 1)?

Shoult pics on miata.net

The expected trigger angles in the 99 decoder just look too coincidental with where the timing dots are in the video

 

Deleted

 

I don't think it is anything in the ignition settings. As I mentioned in the original post this tune worked in my built motor like a week ago.

The only changes were to work on a stock motor instead of my built motor, so: cc's on the fuel settings, rev limit back down to 7200, lowering the VE around idle to not be so ultra rich that it won't run. The built motor is bored out, revs to 8200 and moves a lot more air than this stock one does, so the stock one requires less fuel.

 

I would load a base map from DIY Auto Tune to rule out the programming. If you have a stock ECU, try that also.

 

My only thought is an exhaust/intake cam swap on the donor motor and you're not using the right cam wheel (very unlikely) or you swapped spark plug wires or coil plugs.

 

​​​​​​
The cams have not been swapped, they don't look like they've ever been out of the car. It doesn't look like anyone has been in here before.

Do you really think that after putting in five motors in this car that it could possibly be a coil wire swapped? Really?

 

It's not to tune. The exact same tune that worked just fine with another motor a week or two ago. There's nothing in the tune that could possibly put the timing off like this. As mentioned in my original post tuner studio is reporting 10°.

I'm going to try a different ECU today.

 

Some fun updates from today. I tried a 3rd crank sensor, I tried my old ms2 I had sold, the buyer had not installed it yet and let me borrow it. With the other ecu it is behaving the same.

Another miata friend of my came buy, confirmed all the mechanicals looked good. He had an idea to set the fixed advanced lower.

We discovered the way it is running it will not idle low. So the 1600-1900 it was idling at was deceiving on how well it ran.

We set the fixed advance to -10, with the offset at 20, and the timing marks were close to the correct position.

With it like that the engine was MUCH happier and would idle at 800 RPM.

So, our conclusions today are, mechanically everything is together correctly, and secondly the timing that is shown appears to be accurate on where the timing is at.

 

Did you see my post above?

 

See edit in the OP for solution.

 

I guess this even more common with the aftermarket trigger wheels that don't have the bubble center. Have heard of many that have had this issue with the FM units. Good wheels, just easy to install backwards.