When I try the electric start a clicking noise starts coming from the back end of the bike, I’ve replaced the solenoid and am left with the same issue. Sometimes it’ll start others it just continues clicking. Any recommendations would be greatly appreciated!

 

If the solenoid clicks once when you press the start button but nothing happens, either the solenoid or the starter is faulty, as you have fitted a new solenoid, it is the starter. If the solenoid buzzes, either the battery is flat, or one of the thick leads from battery loose (this includes earths), or either starter or engine seized. On some Yams there is more than one solenoid, so it could be the other one buzzing, same principle applies, except the wires to it are all thin, so finding a faulty wire is harder.

 

and all of that applies even if I can still start it with the pull start first pull every time?

 

Put test light at starter wire an push starter button if light up then your getting 12volts to starter then issues is there if clicks an dont light up then button or solenoid I can give a test for solenoid if you need me to

 

"and all of that applies even if I can still start it with the pull start first pull every time?"
Yes, the ignition is AC direct from the alternator, no battery power needed. The electric start is battery powered. Though a Yamaha pull start that actually works is a rare thing.