When you look at the fuselage, is there any sign of right or down thrust already built into it, or is the firewall straight and level? Most of my planes had the proper amount of right and down engineered into the firewall, so the thrust line is correct and there's no need to tilt or move the engine. My old Phoenix Extra 330 Version 1 is the only plane that did not. Double check your firewall.

With the Phoenix/Seagull kits, it's also possible to use the original bolt holes drilled by the factory to find the centre point needed by the engine so it will line up with the cowl. Usually (but not always) this gives you a spot-on alignment and the cowl fits correctly. However, the paint doesn't always line up... My Phx E330 paint lines aren't even close, but she flies great.