does it matter if i mount the engine upright or will it affect the way the plane flies?

no it won't matter.well it mite throw the cg off for ke flight haven't thought about that. but it'll look like a monkeys but no offense.

Ive got a UCD .46 with a TT.91 4stroke mounted up right on it.
NO PROBLEM!!
CG is fine!!!
And I can start the dang thing w/o the reach around!!
I mounted my throttle servo externaly right behind the firewall with a very short wire with a clevis-z-bend.
works great, just be shure to put your fuel tube over the clevis, it popped loose on me one day!![X(]

I have my Saito 82a mounted upright. Throttle servo, switch, radio located at TE of wing, 4.8V 1100mA battery stuffed just behind TE of wing. Elevators locked with 1/8 dia U-shaped music wire. Hitec 5475 digital (4) on all but throttle. 1.5 oz of lead on tail for balance.