Funnily enough, I bought a similar bike a few years back - 125F motor in a 125E frame. As a race bike, the other way 'round would work better, but meh...
The YZ125Es are a sweet handling bike with no impossible to buy parts and no real trouble spots - they're hugely under-rated, simply because they're too new for pre-78 racing and are outclassed by most of the other Evo-class race bikes.
Airboxes are hard to find (dunno why people are so keen to rip them off), I've seen one cracked frame (around the top shock mount/down-tube area), and the footpegs can come loose (occasionally wrecking the splines on the frame, but usually falling off first - and only if you completely ignore the many warning signs), but that's about the limit of the likely problem areas.
If you just want a bike to ride around, many bits are the same as monoshock DT125/175 so they are a common source of cheap parts.
Between Viper666, Mainline, DG26, myself and a few others, there's not much that we can't help you out with.
These links will help:
http://yz125f.blogspot.com/http://yamahayz125e.blogspot.com/Scott does top quality, very authentic restos - so if he says it is so, then it is so! He also makes very good reproduction mudguards and front number plates.
except me of course, I don't know what I'm talking about
Sigged!