gears

When you get your new valve installed drop me a line before you crank it over - ALWAYS check your cam timing 3 times before starting the motor.

Not likely it's the springs - the only way they'd go "bad" is if they're over extended.... because the clutch assembly is worn. When you get it apart you'll be able to see where the friction material is supposed to be, it'll likely be mostly gone or heavily grooved. You might need the drum as well.

did you remove the flywheel when you were doing this? Flywheel has 2 timing marks on it F for ignition and the T is for the camchain.

Great video explaining what happened and what you did. It looks to me that your centrifugal clutch assembly is toast. That's those 4 shoes that engage the drum with the springs you've replaced. You'll have to pull the clutch assembly out of that drum (bend the lock-tabs free on the center shaft of that clutch, buzz the (22mm?) nut off the shaft and pull that shoe assembly out - check the inside of the drum, looks to me in your video that the clutch & drum are so worn that the shoes are moving excessively and that's whats breaking your springs - they're being stretched too far. That secondary assembly in the lower left corner with the spring, plate and triangle of balls looks like you've got it right - that's what "disengages" the clutch when you shift. Let me know if your clutch is bad, I might have a spare in the barn.

the starter clutch sprag assembly is shot - it's a one-way bearing assembly on the back of the flywheel, 3 or 4 rollers are spring loaded to let the gear the starter engages freewheel in one direction but lock up the other way. You'll likely need a new flywheel and gear assembly - I'd look for a used one cause new isn't going to be cheap.

you have to disassemble that rear U-joint and get it out of the way to take the nut you're referring to off, pull the yolk off the splined shaft coming out the back of the trans and replace that seal (Just did it on my Kodiak 400), then grease the U-joint and put the whole thing back together - something like $15 for that seal (I got mine off ebay - genuine YAMAHA).

it depends on the parts. OB is right though, you can compare via online parts suppliers - OEMs have a part number interchange through their inhouse systems. Beware, sometimes different part numbers are for different paint colors - CB1000 used the same head as a CB900 but it was painted silver instead of black so according to OEM they were not interchangeable.

Did you find a mouse nest anywhere (under the seat). If you pull the LH brake lever it should crank with the start button regardless of the R light being on.

Check your battery voltage - keep your volt meter on the battery when you hit the starter button. Drop of 2+ volts without the engine turning over and you've got a dead cell. Try jiggling your connections at the battery, corrosion there at a tight connection will keep it from starting and cause the solenoid to buzz.

how long does it stay running and how long does it need to sit before it starts again? Check for spark when it dies - could be the stator gets hot and the pickup dies and once it cools off you get spark again. Could be running faster than fuel can get from the tank to the bowl (clogged petcock screen).

With no battery hooked up (even a bad one) you may have fried something electrically - check for spark: pull the sparkplug, re-insert it to the wire, leave the threaded portion of the plug against the motor (cyl head) and have someone pull the pullstart - watch for a fat blue spark that goes ZZKT. No spark try a new plug (NGK D7EA). Still no spark you might be chasing electrical parts (Stator/Pickup assembly, CDI/ignition box).

Space the Right rear wheel out to clear. Knock the studs out, get some spacer and longer 10mm bolts at the hardware store.

Leave the semi-auto clutch, it's bulletproof. Displacement - you're pretty much locked in. Brakes? I'm right there with you, cable drums are next to worthless, I've converted all mine to hyd disc front and rear - Ebay has lots of parts that will swap in, most of the yamaha hub/discs will fit the rear splines on your right wheel - I use a big bear front hub/rotor with a honda atv caliper on the rear of my kodiak and the wife's timberwolf, any rear MC will work, mount it to the frame and connect it to your stock pedal. Front brakes I look for something with the same bolt pattern and get the whole hub/disc and mount warrior calipers (they're cheap and dependable), again, any MC will work up there on the bar - wrecked sport bike MCs are cheap with rash on them. Good luck!

any noises? grinding crunching popping should steer you right. If no noise and it's spinning off the ground maybe the 2ndary clutch is hung up or you left a friction or steel out of it so that even with the springs fully engaging the clutch basket it slips. IIRC there is an alignment mark on the inner and outer clutch basket that might be your problem.

Fouling could be from running cheap plugs -ie running to wally world and picking up a champion that "fits" rather than the correct NGK - also air filter/box could be packed with critter nest - that'll cause it to run rich and foul frequently (I always put a screen into the intake snorkel behind the tank to keep critters out).

I'd imagine that the cylinder head mount is a different size but the driveshafts should be in the right place and bolt up. Run the 350 carb and wiring/cdi.

that free case of oil may have cost you your clutches....

You've got 2 clutches in there - the clutch pack and a centrifugal clutch (that's why you don't have a clutch lever for starting or shifting). Spinning hard left would cause the oil level on the Right to increase.... maybe enough that it immerses part of the centrifugal clutch - causing it to slip? And yeah, I don't think the automotive oil is helping - it's got friction modifiers for engine parts that don't get along with clutches (which need friction to work).

that was common on stators from Rick's Electric - I know on my RZ the wiring switched OEM between years, maybe the aftermarket one is the same physical unit across years with that wiring reversal.....

that switch is activated by a detent on the shift drum (IIRC) the hand brake (on the left bar) is a safety over-ride allowing you to start it in gear. If neither one is letting the electric start operate then you could have a bad ground to the neutral light or a bad solenoid, or a bad starter, or the start switch is bad.....

I'd plow in 2nd gear with that machine - the wheelspeed is key to moving the snow. 1st and you'll rev the crap out of it.

a 4x4 truck socket fits that special nut - and it has LEFT-HAND threads.

yeah, sounds like a full carb clean is in order - too many people think yanking it apart and spraying it down is the same as a rebuild. Make sure the pilot jet is clear - if you don't have a jet cleaner set (K&L makes a nice one) a single wire from a wire brush is typically small enough to poke through.