Bad fuel pump? Sometimes the pumps will start to fail like that. I had a similar issue with my 690 enduro and it was a poor connection to the coil. Could be so many things though.
2009 KTM 690r Enduro in da house
2002 RC51 SOLD
2010 KTM 990 Supermoto R traded due to immobilizer problems:(
2014 KTM EXC 500