I've been having the same problem with my 2009 TE250, where did you buy the replacement pump? I checked the dealer and the OEM pump is pricey, $642...
Here's one a little closer to Texas: http://www.ebay.com/itm/13-Husqvarn...ts=Make:Husqvarna&hash=item2c7d8d36ae&vxp=mtr Or you can go this route: http://www.ebay.com/itm/Intank-EFI-...Parts_Accessories&hash=item2eca2d433f&vxp=mtr I have no connection with either of these sources, I just did a search on ebay motors for "husqvarna fuel pump".
I had mine rebuilt for around $200.00 all in. I just dropped off the bike and picked it up when done. The whole pump likely does not have to be replaced.
Well it turned out that the relays were not at fault in this instance. So I dropped in a new fuel pump and problem solved. Interestingly the fuelling was really crappy for the first half hour of riding on the new pump with lots of flame outs etc. After numerous stops and starts the EFI eventually sorted itself out and bikes running great now