That plane originally had an OS 120AX mounted on it. The bottom cutaway is to fit the big box muffler. There are pics in this thread if you want to see it. You will need to cut out some to fit around your muffler, and also to make sure the cowl fits around the fuse/firewall - it's a tight fit.

Also, the engine was pushed back closer to the firewall to help the CG. Because of this, excess material has to be removed from the bottom to allow the cowl to spread out a little.

Making a template out of another cowl doesn't work as easily as we'd like it to, since they aren't made to stack that way. If you do it that way, make sure you cut inside your lines, fit everything up and make adjustments.

I wouldn't worry too much about cutting holes for cooling until you've got it properly mounted and tested out. You can always cut more later, but putting material back isn't easy.