Got this bike running 2 months ago after sitting for 15 years.I rode it a few times a week in that two months no problem.I went to start 2 weeks ago and nothing but pops.There is smoke from the header and the exhaust,carb has been cleaned,has strong spark,and fuel has been changed(40:1).I'm not sure what the problem is but it rained all afternoon and the tarp was blown off when I got to it.I called a mechanic and he said possible crank seals and my buddy was stumped and just said carb.I have no idea what this could be.Any ideas?

Yep i'd say right side seal has pushed out.
Will be obvious to see if you pull the cover.
Could be left seal but lots of smoke points to right side.
That can happen if it gets a belly full from a carb float valve fault if fuel has been left turned on.
Or water if plug is out & parked in the rain for a long time.
Could check the flywheel crank key in relation to the back firing but if it was running ok before i think i'll stick to the right seal "guess".
Welcome from NZ if you're new.
On rethink i might reinforce checking the flywheel key or see if the nut feels tight at least which will give an indication.
Puller it 27x1 thread pitch lefthand thread. Most common puller on the plannet for just about any yamaha flywheel.

I did have to take the clutch off when I first got the bike running and I have a bad habit of leaving the fuel on.My guess was just it running after 15 years,I've never had to work on crank seals before.

www.amazon.com/Motion-Pro-08-0026-Flywhe...r%2Caps%2C303&sr=8-1
Just lost my text while writting damn it.
Yep clutch basket has to come off by memory as crank gear won't quite clear the basket.
The seal retainer will be bent out too but just push back.
If i was desperate to get it going in the weekend i might just try to push the seal back in without undoing anything & push the retainer back flat & with plug out & ignition OFF just push it around to expell fuel--exhaust off too maybe.
Then see what gives.
I have a very similar bike which was a magneto model AT1 125 from 1970 but nowdays with a 175 top end.
I shouldn't be teaching you all my bad habits lol--but--See how ya go.
ps again, if you push that plate back just check the 8mm philips head screw is tight, just incase!!.
I worked in the Yamaha workshop localy through those fun times. Bring back the "70's i say!!.
Well i guess we're reliving them through this forum which is cool.

images.cmsnl.com/img/partslists/yamaha-c...gyau0828a-5_d6b1.gif
I can't find the retainer but here it shows it on a CT2 #25 & # 24
images.cmsnl.com/img/partslists/yamaha-c...gyau1118a-5_d975.gif
Even with the retainer they'll still push out if the case is full of fuel as seals just get tired of hanging in there but are still ok sealing on the shaft.
Could fit two retainers if desired as the threaded 8mm holes are opposite each other & used for the case & crank puller--pusher.
Just be careful the head of the 8mm screw or a bolt you might use doesn't touch the clutch basket gear if you add a second retainer.
Anyway, a new seal will stay in as will be tight without needing a retainer but think i'd still oil the seal outside plus the case to help it slide in so as not to grab or get damaged.

If plug is wet with fuel it might just be flooded.

Hey Mark, i go for the hard jobs first haha.
Like get the motor apart then find its out of fuel.
I'm working on a quad Eiger 400 from a local horse trainer.
Making the worst detonating sounds big knocking etc & smoke--strange smoke.
Was looking at ignition over advancing & all the hard stuff as that's how it felt.
Turns out they'd poured something "horse" into the fuel, not diesel but smells off but looks like fuel so mixed good but froths big on shaking.
By that time i had the bike half apart damn it. Clean fuel & perfect again.
Then had a squeak when pushing along.They weren't worried about that.
So i Jacked it up anyway & the wheel with axle fell out haha.
I'm past working on all this crap but they live too close to escape.
Sorry, i shouldn't be clogging up this post with my rubbish but links don't take up much room i hope.
photos.app.goo.gl/vXmXgc6h4NMSgXRz7
photos.app.goo.gl/PynA9o94sy8EsaiT9

can you say"wet ground"