Well your problem is quite obvious...
You must be working on a Chinese knock off unit, because we only work with
Kubota's around here!
Why did you do a Cylinder head replacement?
Does it overheat?
Did you do a compression test before or after the cylinder head replacement?
Where did you get the injectors from?
Does it smoke when it does this?
And if it does what color?
Does it bog down or just low RPM?
Have you checked the air filter and housing?