04 Yamaha wrf 250 irratic revs

I recently picked up a 2004 Yamaha wrf 250. I bought it blind off eBay and had it couriered to the house.
It had been standing a while as was sold as a non runner. When it got delivered I was really happy with it, condition was great and with the carb stripped and cleaned it fired up. I ran it briefly, switched it off and tucked it away.

It's been sitting a few weeks but I plan on getting it mot'd this week. The bike was a pig to start, so I got fresh fuel and redone the carb. Cleaned through and it's spotless. The bike starts on choke and will run but the revs with choke on seem high. With the choke pushed in, the revs do not drop a great deal and then after around 30 seconds it will idle ok and sound normal. If I Rev it from idle, the revs hang on a touch, so I need to adjust the mix screw on the base of carb. But I can't get my head around the initial sky high revs on start up and why the revs stay high for a long time after the choke has been pushed in? It could of been like this when I first started it weeks ago but I only ran it for a few seconds so not sure.

Things I've tried; recleaned the carb, adjusted throttle cables, greased hot start valve and freeplay on hot start lever.

The bike is standard other than a fmf end can.

Unscrew the choke pull it out and clean it. Had this problem before on a WR. The choke was staying on even after I'd pushed it in.

Hello Steve, I've pulled the choke plunger and hot start valve and cleaned both. But worth rechecking the choke if it's a known issue.

Today I've pulled the carb off, radiator and checked the valve clearances. Something is not quite right with the timing.

With the bike at TDC and the flywheel mark lined up, the notch on the exhaust cam is slightly above the headface and the intake cam is around 2 teeth off the mark. The cam lobes are roughly pointing away from each other as stated but no matter how many times I rotate it I cannot get the intake cam to line up on its mark.

I've been watching a few videos on YouTube and one bike with a very similar timing issue was due to a stretched cam chain. It had jumped 2 teeth, causing difficult starting and loss of power.

My bike is difficult to start, can't comment on the power as I've not ridden it but think I will buy a new cam chain and look to replace it.