Thanks. Its fully up and running now. Just need some odds and ends and some tires that are close to the right size. 
 

Can anyone speak on gearing?

I finally got her up and running and got half a block before the chain snapped. The gearing seemed crazy low (guessing its stock). Didnt really get to fully test it out, but first gear seems super low. Has anyone up a tooth or two in the front or down in the rear? 

Yes, with many of the old Yamahas, going a tooth more in the front or two or three lower in the rear will get you more top speed. BUT. Often not the case with the 125cc bikes. What's your red line? Because the 125s will rev so high, and because they make more power at the top end, it's often advisable to go one tooth lower in the front to help keep the revs...and the tops speed...higher. Counter-intuitive, but Capt.Dave says it works. And if you have somewhat to more than somewhat hilly terrain you'll save a lot of downshifting, too.

First step is to count the sprocket teeth and find out what you have.

Also, if you broke the chain, what condition are your sprockets in? Usually the same condition as the chain!

You actually snapped the chain?
Or did your master connecting link open up and separate?

I studied chain failures years ago...  got to speak to some industry experts.  Rust will absolutely kill a chain.  The plates and pins have a ton of science and precise hardening...  outside has to be hard for wear and strength but can't be too hard or hard all the way through or will be brittle and can't handle shock load.  Just a little rust will cut the strength in half or more if it damages the case hardening.  I actually tested this in college by taking a length of new chain and failure testing it...  and testing other lengths from the same roll of that same chain after letting it rust. 

New chain under extreme stress bent the pins and basically the press fit/staking failed and the pins pulled out of the side plates at very high load. 

Rusty chain failed at much lower load and usually snapped the side plates.

I didn't test master links but they are usually the "weak link" and will fail first. 

Developed a method of building chain that involved silver soldering the pins into the side plates. This increased the strength tremendously but was too expensive and impractical. 

Tsubaki X-Lambda Chain is incredible stuff. We use it on conveyors that are used in extreme conditions. I wonder if they make it in the size for our Enduros....

tsubakimoto.com/power-transmission/drive...ee/lambda/long-life/

MarkT is right. There are a ton a side plates with cracks. 

 

As far at the gearing goes. Im asking if anyone has re geared one of these bikes for higher top speed and what the experience is like. Counting teeth doesnt really help me figure that out. 

Umm...  I would not call that bike "geared low", you say it is.  So the first step is to see if you have stock sprocket sizes which means counting teeth.

Or just buy original sprockets I guess?

Mothersbaugh already shared the wisdom on that model that going a little lower on the stock gearing actually will give you a higher top speed.  In other words, it's a mistake to gear that model taller than stock.  It's not that powerful 

Of course you could make the power situation better by swapping to a 175 top end.