Well, the only way to fit that fourth bolt on the motor mount to the firewall would be to slide the engine forward on the mount. Sounds like a pain by looking on the pics you have already drilled the mount, but that's the only solution I could see moving it forward. Again, it'll only be a few millimeters and I doubt it would hurt anything. I do like your idea of installing the cowling and looking at the spinner backplate, you probably want about 1/3 or 1/4 inch clearance for the prop. I you would like I could measure mine on my Cub.

As far as the cylinder sticking out,,,that's what the full scale plane looks like. Might solve your throttle cable/push rod problem.