It looks to me like you need to be taking more off the bottom side of the door sill. The fuselage side skins aft of the door opening should fit right in that joggle that is molded into to the bottom of the cabin top. I had to sand a lot off that bottom side of the door sill to get the top down enough to fit in that joggle. if you measure the height of the side skin from the longeron to the edge (like a half to three quarters of an inch), that should be about the same measurement as that joggled area on the canopy (where all the countersunk blind rivets will be).
RV-10 Empennage- Complete
Working on windcreen
On it's Gear, Engine Hung, Prop On