Tearing down my 800 twin for the crank bearing upgrade. Noticed the slot in the end of the water pump
shaft that drives the oil pump is not a straight slot anymore. It has been hammered on the load sides and is probably 15-20 degrees from being a parralell slot on both load sides of the slot at the OD. This is a tough one to describe, I could post some pix later tonight.
I am wondering if any of you are familiar with this, and have run it as is, and it is not an issue? Seeems like there is no way it could slip out and would have to shear completely before the pump wouldn't turn.

Also anyone have a hell of a time getting the 3 stator bolts off to remove the stator/timing plate? Thinking using some heat but don't want to melt the windings insulation. Perhaps an hand impact driver with a LONG 4 mm allen socket? Suggestions?

Yes, have seen it on everyone I have had apart. Just use it unless it is real bad.

The stator bolts are tight but have never had too much of an issue getting them out. Problem with the hand impact or the air impact is twisting the hex shaft but you do what you have too.
Quite often I use a 3/8 air impact with the air turned down

What you're describing with the oil pump drive "tang" wearing into the water pump shaft isn't all that uncommon. Motors that tend to shake more (800s primarily) tend to be harder on the shafts. In addition, misalignment between the centerline of the oil pump and the centerline of the water pump will also make the problem worse, as will a bent shaft, loose bearings, drive gear on the flywheel misaligned with flywheel, even a bent crankshaft can contribute to the problem. It doesn't sound like your shaft is worn too badly - I've got one spare assembly in my shop that must be worn 30 degrees or more. I don't think I'd use it for a long period of time without replacing the shaft. I guess you need to decide how long you intend to keep the sled and decide whether you want to replace the shaft, check bearings etc. As far as the stator bolts, they are often quite tight. It helps to have an allen socket or similar that is long enough to get some torque on them to get them broken loose.

Thanks guys. The hand impact worked real well to loosen the stator bolts.

I think the oil pump drive will run as is, but if it's cheap, might as well get'r'done. But I haven't had a chance to look into replacing the water pump driveshaft (this has taken all the wear.) Is this something replaceable or you need a whole new water pump? Looks like the mating slot on the oil pump is fine as is.

The water pump is a collection of parts, not a complete assembly. You would need the shaft, 2 bearings (or clean and repack them), a new seal and a new gasket for the housing on the back side of the pump. The parts won't be "cheap", so it depends on how badly you feel you need to fix it.

If you are tearing down the bottom end to do the crank bearings, it makes perfect sense to rebuild the water pump assembly while you are at it, especially if the sled has over 5k miles on it.
There is a weephole on the bottom of the recoil housing you can check to see if the seal is leaking.

The mechanical seal on the water pump shaft is a bugger to replace unless you have the proper tool.(#2872389).
Unless you are the adventurous type, take the water pump/recoil housing to a dealer and have them install the new shaft/bearing/seal assembly for you.