I have a question about how the CDI control box functions. Does it change the timing at a certain RPM. If so, does it advance or retard ? If I change engine to 75 DT 250 points ignition system, I would lose this function, Correct ? Would this be detrimental to the Life/Performance of the 400 engine.I installed an NOS pulser and I holed the OE piston. I then installed a Trail Tech cylinder head temp gauge on the bike after a piston replacement and it is going into the low 400s on short test rides. Yes seals have been replaced. Timing has been checked below and over 3000rpm and it does not change. Any help greatly appreciated. 

Timing is retarded for easier starting with early CDI but does not change after that. 

Your point mag will be ok set to whatever it is --think 2.9btdc on a big motor. Just be sure your de-compressor is working off the kick start & kick it good & hard from the top 'against compression'--not after it & follow through until lever stops on the footrest. She'll start first kick--on a good day.
Later model DT400 cdi mags had a good pulser but the early one seem to suffer. They just retard to kick then go straight to advance--say '2.9' & hold.

Is 400-430 too high for cylinder head temp ? swapped gauge to my dt 360, saw 300-350.

I have a dt360 the highest the head temp has been was about 370 but usually around 350.

Need more info.  Are you just cruising around and seeing 400-430F on the CHT?  Or is that from a full throttle run? 

That temp is about the hottest most people I know like to see under heavy load like full throttle for non-competition use.  The challenge on an engine you don't have "history" with is that head temp climbs relatively slow, so if you have an unknown issue and try a full throttle run, by the time you see a 430F temp it might be too late and the gauge may continue to climb to 500F or more as you coast to the side of the trail.  (Been there, not fun)  Best to sneak up on it...  more below.

You said you checked to see if the timing moved when revved...  did you check to see if it's correct?  I like to time the 360/400 at 0.100" BTDC which is retarded a couple degrees from stock...  With standard points (where timing doesn't retard for starting like a CDI does) they start easy and run just as good everywhere else. 

Also, new seals is not equal to "no air leak".  Even new manifold gasket joints to reed valve commonly leak for example.  There's a lot of places you could have an air leak including a bad seal...  especially if non-OEM single lip seals were used.  This is why I pressure/vacuum test new engines and BEFORE tearing down an engine that failed...  which something I never did until a holed a piston due to a brand new defective seal. 

When I said "sneak up" first is make sure timing is spot on and no air leaks.  Next is ride it, and get baseline temps.  Yours are on the hot side so I'd jet richer.  Note that jetting the carb has to do with throttle position, not RPM.  See Mikuni jetting charts and adjust the circuit in the carb that corresponds to the throttle position.  (i.e. installing a larger main jet won't affect the mixture much at around 1/4 throttle if that's where you're seeing the 400F+ temps)

Thanks all. Sounds like my problem is down to jetting. We (all of you) have helped me eliminate the expensive/rare ignition components from the list. I will refer to the Mikuni tuning book and find my way out of the darkness.

Bear in mind, if you are using ethanol type fuel, your jetting requirements will be significantly different to fuels with a higher calorific value.

Check to see if your carb is fitted with stock size jets. If it is, go up 2 sizes on the main, and give it a try. There may be issues in transition stages, but getting the main correct is the first step.

Where I live, all we've had E5 for years... now a lot of E10. Non-ethanol fuel is not commonly available.

All my stock bikes (including a DT400) are running stock jets with the exception of the 1980 and 81 DT175's with one size up on the pilot jet. The pilot on those last 175's before they couldn't meet EPA standards was lean. They run fine on the 22.5 pilot, just idle a little better with a 25.

Storing a bike with ethanol fuel that hasn't had a good fuel stabilizer added? Not a good idea. But they run just fine with stock jets on the available E5 and E10 ethanol fuels we have in the US.

Temperature and altitude are far more significant factors that may require rejetting... and of course air leaks.

Fuel with lower calorific value, means the need for more fuel, to produce the same amount of power, as a higher value fuel.

An extreme example would be an engine running on methanol. These are likely to need jets around 2.4 times bigger than using petrol.

Its very simple to fit a bigger main jet, hopefully it will sort the problem, but if it doesn't then not much lost.

The other thing that would be well worth doing, is to check the ignition timing with a strobe light. Not only will that indicate the firing point, but it will also show if there are any issues with spark breaking down at higher rpm, and if there is any obvious timing scatter.

Like changing the jet, it's quick and easy, and could save a fair amount of time and money, if there is a problem with the ignition.