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Yes, bikes of this vintage are no longer plug and play when it comes to parts. You'll have to do some research and piece it together. Part of the fun if you ask me.

On the older bikes you have to be a little more creative to find all the parts. That motor is a mix of parts from the 80s into the 90s. ProX, Woosner, Vintco make rods and main bearings. Pistons you can find ProX, Wiseco, some OEM on ebay. 89 is still an iron bore. Transmission bearings you'd have to go OEM but Yamaha is well known for just reusing parts from other bikes so they should be available Mitaka makes an outer clutch basket but for inner your going to have to find an OEM. Couple companies make clutch plates...

Wossner make a conrod for this bike, # P2048... https://wossnerpistons.com/products/p2048

It has nothing to do with it opening or closing. If the valve was trimmed for the bigger bore it is no longer the correct size for the smaller 250 bore. Post a pic of the inside of the bore, the exhaust port area with the PV fully closed. Notice how this is designed to fit very close to the piston. If yours was machined bigger for the bigger 300 bore it will no longer fit close enough to the piston in a smaller 250 bore.

The center powervalve (the guillotine style one) needs to ride very close to the piston and rings in order to hold compression in and properly alter the exhaust port height as it is intended to. Since the 300 bore is about 7mm bigger, the face of that valve has to be trimmed back about 3.5mm for proper clearance. If you then put this valve back in a 250 bore, it will have about 3.5mm of excess clearance to the piston which may allow compression blowby and not properly lower the exhaust port at low rpm's like it is supposed to...

Ignore my needle comment. Forgot the 99 had the PWM carb. Going richer on the oil mixture has the effect of going leaner on the gas to air ratio. Since you put more oil in, there is less gas, per volume. It’s a very small difference from 40:1 to 32:1, but it is a difference.