Project First bike, the FZR250 3LN

BTW - this page has the pilot chamber bungs explained, basically you use a stanley knife blade under the edge to lever them up - be gentle as it's a weird sort of crumbly metal, almost plastic like in it's consistency - once you get them moving upwards you can go to blade screwdrivers

https://www.2fiftycc.com/index.php?threads/fzr250-3ln3-carb-problem.8770/page-5#post-112020

 

That's not good at all, I recall those valve clearances were below minimum spec, it's either the clearances or bent valves if they cams were installed mis-timed at some stage

Compression testers have a schrader valve like a tyre, is there a chance it was stuck closed, rubber stuck to the metal and unwilling to budge and needed a press to free it up?

Oil down the plug holes next to test the rings

Not sure what I'd do first, clearances or check for bent valves

FWIW - the cylinder head isn't difficult to remove and new OEM gaskets are available for about ~$35 which isn't expensive

IIRC correctly I got mine from these guys, express post - no issues - currently listed as available in Australia which is a good thing, so the local Yamaha dealer should be able to procure one for you

http://www.firstclassmotorcycles.com.au/part/yamaha/3LN1118100#content

 

Well the cams have a small casting on them 'IN' and 'EX' - I suppose they could be in the wrong spots - on the RHS facing forwards between pots 1 & 2 from memory

 

Well with cylinder 1 firing that cam should be pointing outwards as it's just inhaled and should be preparing for the exhaust to open, so that cam should be preparing to push down on the valves

Not sure if the valves can clash, but they won't be bent as the timing itself if correct, just the wrong valves moving - it's been firing a spark at the point where the valves are both just sneaking open during the overlap point between exhaust stroke and intake

I don't think they will be bent, and it pretty much explains everything you've been experiencing, and it's a quick fix

 

OK just looked at this pic - those cams are in the wrong place, those lobes for cylinder 1 intake are for the upcoming exhaust stroke on that cylinder - now that I think about it, the 'IN' and 'EX' are cast between two cam lobes.

Just swap them and then check the clearances and it should go VROOM

 

So glad for you, no wonder it was a total mystery

Do the seals in the carbs and you've actually been across many of the settings, fuel level is most important, then you have the balance and pilot screw adjustment which usually happens in tandem

 

The rest is easy, it's checking things mostly EXUP valve, balance carbs and adjust pilot screw, I forget if there's a gasket underneath the water pump, if there is, you can buy gasket paper and cut your own, it's always a god thing to have to hand anyway - comes in various thicknesses

If the coolant has been sitting all of that time, worth changing and you can put a portion of vinegar ~25% in distilled water to run through as a flush
One thing important to know is that there are two coolant system bleed screws on the cylinders to get residual air out.

 

Surprised it ran at all without the airbox, with that in place I think you'll find it's much smoother

For what it's worth the transmissions make a lot of noise also, they sound like a bag of spanners but that's normal - likely a big part of the noise you are hearing

 

It might be sufficient to remove the water pump cover and gently clean the mating surfaces then reassemble