At idle, it might fire a couple of degrees retarded.  By about 2000 RPM, the marks should be perfectly aligned when using the timing light. 

Several DT400's have had the CDI's go bad in a way where the timing is firing advanced.  Seems it would have to be the stator but I'm not sure.  One member had a shop re-drill the stator plate to get the timing right.  Not sure how long that worked as it seems something was bad/failing. 

Stretching thoughts beyond reasonable, if the center boss has ever been Re-riveted i guess if not back in the same holes [na that'd be more than a little bit out]. Only thinking along those lines as by memory the pulser is fired by a cut out along the center boss, so activated under the pulser not across the top. Don't dwell on that thought & could be wrong. I'll go look later in my manuals.

That seems strange that these can fail with the timing being really advanced but if its happened to others that sure seems like what's going on here. I uploaded some pics here, does anything look out of place?
imgur.com/a/RQNQ3Y4

If not then I guess I need to fit a replacement ignition. I know good CDI parts are hard to find and I don't know if this is a CDI unit failure, or the pulsar coil, or stator... So given the uncertainty with what needs replaced I should probably just get a whole new system? Does anyone know a good budget friendly replacement, or does everyone just do a Vape system and convert to 12V? I've done that on an RD250 with good results but I don't plan to keep this bike very long (I have too many others) and just want to get it running right before sending it off to a new owner.

Just stretching the imagination would some sort of diode or resistance added to the advance wire be it green white or red white as an artificial delay tactic, make it fire later trick. Be interesting to mark TDC on the flywheel then spin it with a drill & strobe it with plug out & earthen to see where it's firing at starting speed. Then if you think that imaginary mark is a bit advanced from where you think it should be for starting then just retard the stator  move it anticlockwise. Maybe I'm talking rubbish lol. Good at that.

This might be your answer if you just want to get it running to ride a little or sell:

"One member had a shop re-drill the stator plate to get the timing right. "

You've already figured about how far CCW to rotate stator.

I'd let a buyer know it may need a new ignition if you go this route and it works.

I thought about that but its such a nice bike (its in really nice shape) and that seems like a kludge fix. I just hate to do a fix like that on a nice bike, though it is tempting. If only I had another DT400 sitting here to swap parts with to at least narrow the issue down to the CDI unit or pulsar coil (I can't imagine the rotor is the problem). My other old Yamahas are all points ignitions. Who's near Cincinnati with a CDI bike?

Thinking more on this... I've been thinking I'll put a Vape ignition on my RT3 eventually anyways. It runs fine but I like the idea of easier starting with the Vape. Has anyone fit a points ignition from an earlier model onto one of these early CDI bikes? If that's not too heavy of a lift, maybe I'll put the Vape on my RT3 and put its points system on the DT400.

I swapped to points ignition on my DT360A and DT400B. I used stator and flywheel from two DT250Bs. They are extremely hard to find now.

I've used a 74-on 250 points system on all of my 400's over the years

73 and earlier points flywheel are bigger OD and won't generally fit into the smaller 74-on case opening.  Though some have reported "making" an earlier ignition fit...  likely requires machining of the OD of the early flywheel or grinding inside of cases for clearance.

2.5mm/stroke length x 360 = deg BTDC? Someone check me. I'm tired right now.

Need to use trig or an online calculator.  Unfortunately it's not a simple calculation due to con rod angularity factor.

From experience, the answer will be very close to 20 degrees.