hello,
the chances are you have the timing set wrong, the xs250/400 are terrible for needing acurate timing and I have had many problems from the timing on my 250se being just slightly out, set the timing by ear, not by strobes because it never works on these bikes. Could also be that the carb inlet manifolds are split, new ones are easy to get and are cheap on www.ebay.com with little postage to the uk.
good luck
richard