Clogged or malfunctioning injector? It sounds like you've narrowed it down to fuel, so I would continue down that path. Start by checking its fuse: https://www.manualslib.com/manual/582263/Yamaha-Wr250r.html?page=76 Also check the electrical connection for the fuel injector. I would run through the diags too: http://wr250r.com/articles/diagnostics-mode
Lee