Rangerman...........performance wise mounting the engine sideways is much much better. Mike went half way and it works for him. The majority of Ultimate owners mount the engine on its side. I think you're worrying too much, just build it and fly it. You'll be better off with the engine sideways, as most of the guys suggested to you. My Funtana Saito .72 4/s is mounted sideways, and my lateral balance was only off a fraction. Mounting your Saito sideways, is much easier to reach the glow plug, your high/low speed needle.

I also have a 3D profile (Burrito) again it has a Saito .72. and it is mounted sideways. Excellent performance.
My Waco bi-plane the Saito .91 is mounted vertically. The cylinder sticks out just a little, and when it is up there you can't even notice it. I just went with my feelings. The safety of the aircraft and performance is more important than cosmetics. If I wanted to install it sideways or inverted, I would have had to modify the engine mount railing to keep the same engine trust line. Inverted my engine trust line was going to be out by 1/4 of an inch. It was important for me to build it as shown on the plans. The mods I did to have two servos on the wings instead of one servo and bell crank which I eliminated. Other Mods interplane and cabane struts, aileron pushrods. I used the aluminum airfoiled kind and replaced the crappy hardware that was supplied. If you visit RCSCALEBUILDER.COM and click on Pica-Waco 1/6 thread.........you'll see that bi-plane during the building process. That thread is over 97 pages long, but very interesting.
You'll be fine.
Charles.