Hey guys, back again. Let me present this issue in the best order I can:

Firstly, one day I noticed my coolant reservoir was a lot lower than it used to be. I kept an eye on it and over the next couple days it worked it's way down to empty, even though I hadn't ridden it. I bought a set of handle bars plus some other goodies and took it to the dealer up the road to have it all installed. I also told the dealer to top off the coolant and told them to raise the front wheel 2-ish feet off the ground so as not to trap air in the system. I got the bike back and payed close attention to the coolant level. Again it quickly fell, working it's way back to empty over the next couple days.

I then ordered a water pump replacement, thinking this would solve my problem. Over the weekend I strip the bike down and replace the water pump. Now upon initial tear down the radiator was completely full of coolant even though the reservoir was bone dry. My old oil also isn't all gunky and my oil filter isn't crushed (typical signs of a bad water pump from what I've read). Struck me as odd but I kept going. Everything goes fairly well and I use my new jack and some friends to lift the front of the bike up in the air to refill the coolant. Well my buddy (not a mechanic in the slightest) accidentally over-fills the reservoir and under fills the radiator (me and everyone else were focused on holding the bike in case it fell). The bike was already lowered when I over-looked everything and realised his mistake. I told him don't sweat it, it'll correct itself once I start riding and the coolant circulates.

Aside from a couple of very small drips everything looks good. I go for a ride and to my frustration the bike's temp gauge goes up to it's normal half way point...and keeps going up It does not however over-heat. Instead it just hangs around 3 or 4 bars below the max. So I ride a few miles away and pull over at a shop and let the bike idle. I see that the fan is NOT on even though the bike is running hot. I think to myself that I have a busted thermostat. I shut it off and let it cool down for a little before I begin my ride home. Upon my return and I look everything over again, I see that again the fan is not on even though it really should be. To my horror I find that my coolant reservoir is completely empty again!

What's up with my bike? If the fan isn't on I assume that the thermostat didn't open and if it didn't, the coolant shouldn't have moved anywhere...right? At first I thought I just had a bad thermostat but has anyone else had these problems? Again the small leaks I have are a drip maybe every 20 seconds, not exactly a leak that would bleed out an entire reservoir in a 20 minute trip. And from what I've ready on here, if there was air in the system I would definitely know about it.

Lean the bike over on the righthand side and take the oil filter out. If its wavy, coolant is getting into the oil. If you've ruled out the water pump it could be a cylinder head gasket. DId the bike run really hot for a period before you noticed? The original problem could have been the water pump and maybe she got hot and a gasket went. Did you put tape over the end of the water pump shaft when you fitted the seals? The sharp end can damage the seals as you slip them over and allow water through again. First thing I'd do is check oil filter. Take a pic of it and post it on here.

Yes I taped the end of the shaft before pushing it through the seal (sounds terrible I know lol). The old filter wasn't really wavy, it had a single gap in it. I don't recall seeing that in my previous oil changes but I can't be 100% certain. It's never run as hot as it did today, but I'll look into the head gasket anyways. I should have a milk shake sitting in my air box if its a head gasket, correct?

Didn't manage to tilt the bike over since I was by myself, but a close look around the engine and I found a small drop of "milk shake" coming out of the rear cylinder valve cover gasket To me, this is a big indicator of a blown head gasket. My bike has been running mostly fine so far, I'd say about 90%. I even had to do a full throttle run today to avoid being run into by a car, she pulled great with no complaints. It is ok to ride to a dealer? The closest one that will mess with KTM's is about 30-40 minutes way, mostly highway. Anyone got any idea how much it'll cost?

It's gonna be expensive... I'd say at least 4 hours of labour.
Did you try to change your radiator cap ?

Check your radiator cap or actually buy new one, even if it looks fine. The rubber gasket might be naked and boiling point of the coolant is lower than it supposed to be. It won't cost you much, worth to try.

Ditto - have replaced mine at least three times they loosen up to a point where you only really notice it when you fit a new one.