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Case 1/2's leaking.

If you are burning trans oil, your RH crankcase seal is leaking. Not going to cause the low compression. Make sure you check surface finish on cylinder wall, ring end gap and piston to wall clearance.

Get the head welded, fixed and have them set the squish for your set up. I buy torn up heads for guys all the time and have them rebuilt with different ccompression and corrected squish if i have their cylinder on hand. That way they can test a better head and a basic stocker. 2 stroke heads unless cracked are almost always better to rebuild and set up to your bike.

Every time I want to get a new scoot, I look at the price of their parts and I stick to mine... lol. Not sure how Honda keeps their part prices so low, at least on the older bikes, but glad that they do. Check on some KTM parts and it will make your Yamaha parts seem like a bargain...

Off topic but Honda sells a brand new complete OEM crank for a CR125 for $222... Love my Honda. lol

I'll second this. Great product and completely forgot about them. After that you can go my route each rebuild and just replace the rod/pin at a local shop.

This is your YZ-125? Wossner does a complete crank for $254.00. https://wossnerpistons.com/products/cs2018 That is a great price and a quality product. I would go this route myself.

I'd contact Crank Works: http://www.crankworks.com/ They will be able to discuss options they recommend based on your situation - and they likely have parts that are hard to find that can simplify the repair.

In that case, I don't think you can buy those separately. I think I recall Nihilo making replacement suffers, but only for KTM. You can try giving Hot Rods a call to see if they can sell those separately. They're only there to decrease volume in the crankcase so do with that what you will. Guys have reused them and guys have replaced entire assemblies because of melted stuffers. If you wanted to go with an OEM crank, they are in stock but pricey. You can even buy crank halves and upgrade the rod to aftermarket. I guess a few...

Buy a rod kit with lower bearing, find a local machine shop to assemble and balance. Worst case you can send it off if there's nobody local to you. No need in buying 2 big chunks of metal that are virtually indestructible.