Hard to figure why the pin/bushing is riding high up on the sprocket tooth, after a new undercarriage install, it's usually associated with a worn out chain, along with other worn components, where the adjusters are all the way out, chain is loose and does not ride in the root of the sprocket teeth. You say 1 side is doing this, the other side, the sprocket teeth remain square'd at the tip off like when new.
Assuming the sprocket rims are the correct pitch for the track chain, track frames have no alignment or other related issues, I would double check the tension on the problem side, it's possible that it is too loose, which would show a wear pattern like described, a loose track chain is going to ride up high on the sprocket tooth, eventually the sprocket will slip the chain, I ran a Fiat Allis FD 30 that was so worn it would do this.
Another thing to consider is soil conditions, terrain and operating habits.
Soils like coarse sand and gravel can be abrasive, it will accelerate wear more than other soils, not much you can do there.
Terrain, if you are constantly operating on rough uneven ground, or the side of hills, slopes etc. you will notice all kinds of different wear as the track components take more abuse if one side is lower than the other like on slopes, think about the surfaces of the track components that are now pressed hard up against each other while the track is moving, more surfaces of the components now have contact.
If you saw a recent episode of Axe Men, the foreman from Gustafson Logging, was pulling some equipment up the slope with a D8H Cat, when he came to the top, the crawler came over center, onto logs and uneven ground, he was also at an angle. That is kind of worst case scenario, the extra wear is one thing, but he also let the nose come down a little too hard for my liking, came down hard, have an operator constantly do these kind of things and see what kind of problems arise on the track frames, lot of weight and forces at work. He still had that skidder in tow, if the line was tight, could have pivoted him right around, hope he had the seatbelt on too, nose over like that and you'll end up on the hood, saw an inexperienced forman do that early one morning, the stack kept him from ending up over the nose behind the blade.
Operating habits, has a lot to do with wear, spent a lot of time on 977L's and 955's of the same era, loading trucks and lot of other oddball work. When loading trucks I would try to make a gentle K pattern to the pile, turns were subtle not sharp, but if that was all you did, no doubt one side would have different wear pattern, could be a lot more than the other side, it's good to change directions or sides when doing cycle type of work like loading trucks, more preferrable to use a wheel loader than a crawler for this work.
The flat spot on the bottom of the pin, that is the wear area from the sprocket, hard to say whether the wear rate you are getting is normal or accelerated, typically as I remember from running D3's you would get 1200 or so hours on them before you took the tracks off and had a pin bushing turn done to the new wear surface.
You may want to ask Oz Dozer along with others on the ACMOC/ACME forums, might help with some of these specific issues you describe, especially any track frame or component aligment issues, he's also got quite a bit of undercarriage specifications and cross reference information.