Four strokes will do that particularly the XR400 as it doesn't have a particularly high tech carb.
If it still does it when the engine is fully warmed up and you open the throttle not too quickly, I would check the airfilter is clean. Then check you have no dirt or blockages in the carb.
Every fourstroke I have owned will stall if you crack the throttle open fast enough, apart from some modern bikes such as KTM's, Husabergs jap Mx'ers etc, as their carbs (or fuel injection) are designed to cope with that sort of treatment.
You will have to learn to be a bit gentler with the throttle.
This bogging effect has been the subject of much discussion when the XR400R first came on the market., & successive models were supposed to have overcome this with various modifications. The earliest models were said to be the worst. My version is the 2nd version 1997 bike, so from what I read in TBM etc really helped me to sort out the problems that I encountered.
But I would start with the basics & work through the various parts of the bike one at a time rather than assuming that it is the carb or the air filter or the tappets or a leak in the inlet manifold or a faulty spark plug cap. Any of these could give you the symptoms that you speak of.
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