Ok so here's some updates on this frustrating process.
AF1 originally told me if the piston size does not match what was ordered they can do a postage paid return.
Then they told Pro6 that since we're in Canada they cannot do a postage paid return but they will do a return where we pay for shipping. They also included some fine print about how if there is evidence that the piston has ever been installed, such as small scratches, they cannot accept the return. Pro6 said it arrived with the box open and evidence that it had been installed already so they were concerned the return would be denied anyway.
Then AF1 told me they cannot guarantee exact piston size and none of the pistons they have access to will be close enough to fit. They said they want to help me but I went about it all wrong and I should have had the cylinder honed to match the piston in the first place. They also said in their experience you need to rehone the cylinder every time you do a rebuild on this bike, which is news to me but again, this is my first 2 stroke. I thought it was normally just a piston, rings, and gasket unless something goes boom like always happens to me.
I contacted Vertex USA and they told me that is wrong. The piston should be pretty exact. They then told me to contact Vertex Italy because that is the only place that could have sent this piston to AF1 or Pro6 as it is not normally available in North America at all. At this point I never ended up contacted Vertex Italy as I had given up on getting the piston replaced at this stage.
Then I contacted CVTech and they said it should fit and if there is a problem they will fix it. They asked for some numbers from the cylinder which would apparently indicate the coating thickness. Since Pro6 has the cylinder I asked Pro6 to contact CVTech to give them the numbers they need.
This morning Pro6 sent me an email asking if they can send it back to CVTech for reboring. Assuming this would be as costly as the original repair ($400+) I asked them if it would be free and they said CVTech didn't say anything about that. So I called CVTech and they told me that yesterday Pro6 called them and the mechanic was able to make the piston fit by putting it into the cylinder from the bottom. They were trying to put it in from the top but since the cylinder bore and piston are both tapered it can only go in from the bottom. CVTech said this is very common for high performance engines. The rep said when he talked to them yesterday everything was good so he was confused as to why they would waste time and money sending it back to them if it fits now but he will rebore it for free if it doesn't fit. Apparently this normally only costs $30 anyway so I was worried about hundreds of dollars for no reason.
So I called Pro6 back and they said they have never seen an engine with a tapered bore and that yes, they did get it to fit yesterday (this is the first I had heard this) but they were concerned that the clearance is too tight. Apparently the clearance is minimum 0.0005 inches and maximum 0.0011 inches which they think will cause it to seize if they put it back together like this.
I did some research and apparently nominal clearance is 0.02 - 0.035 mm which is 0.00078 - 0.0014 inches so it does sound a touch tight.
I told them CVTech thought it was fine so to call them back again before sending it to them because if CVTech gets the parts and says it's all fine they'll just send it back to Pro6 and I'll be out like $60+ in shipping the damn thing back and forth and almost 2 more weeks of not riding.
Overall, not too pleased with any of the players in this game but it looks like things might work out soon.