With any custom project, you have to start with the wheels. Get your rear wheel mounted up good and straight. Next, place your motor on the frame, but don't bolt it down. Get a ruler or a straight-edge, and set it against the clutch gear and the rear wheel sprocket - make sure the ruler is flat against both. Mark where your engine sits, and if you can get to them, where the bolt-holes go. Set the engine aside, drill your holes (maybe go a bit oversize for a wee bit of wiggle room, just in case), then mount it up and bolt it down. Cut your chain to fit - as someone else pointed out, don't mix and match chains and gearing, keep it to one size, period. If you have a #35 sprocket, make sure you have a #35 chain and front gear. (I believe #35 is the eneral standard for minibikes ....) Some engine shafts have keyways, where a little piece of metal slides into a groove on the shaft and into the gear to hold it in place.
I've used the straight-edge idea a couple of times - I have a metal ruler on a T-square (another important tool for building straight frames). It's saved me a lot of headaches and broken chains.