This takes time, don't rush it!

Start with the muffler off. Place rolled paper towel in exhaust port, carb intake, over needle valve fitting if/when you remove needle and cover/plug all fuel lines. Install the prop drive washer and hold it in place with the propnut and a homemade spacer if necessary. If you will be using a spinner, the backplate of the spinner will rest against the drive washer, so now is the time to determine clearance between spinner and cowl. Measure from slightly behind the front of the drivewasher to the center of GlowPlug. Transfer this measurement to the cowl and drill a 1/8" hole.

There! Doesn't that feel better? You finally made a hole in the blasted cowl!

Measure the diameter of the cylinder head, then center and mark accordingly on the cowl. Using a hardwood block to "Buck" under the drill bit, drill a series of 1/8"holes at least 1/8" INSIDE and all around your mark for the cylinder head. You want to drill undersize and bring it up to fit with a Dremel sanding drum. (Or hand file and coarse sandpaper). Before you sand up to fit, you will need to "connect the dots" with a # 11 exacto blade, then sand.
Line the cowl up by eye looking down from the top of the fuselage and from the side. You can determine where to place a starting hole for the engine crankshaft. Again, open it up a little at a time until the hole is in the correct spot and of the correct size.

Measure, mark and continue for anything else that the cowl has to clear. Remember that you need access to the low speed mixture screw also.

After you get the cowl over the engine, place the muffler up to the cowl. You can then eyeball where to place your beginning 1/8" hole, then open it up a little at a time until the muffler fits. Usually, when the cowl clear's the cylinder head properly, room is there to install the muffler mounting bolts.

By beginning with smaller holes as compared to big ones, you can adjust the position of any opening as you test fit the cowl, so that when you're done, it all lines up!

Be careful about the dust you create...it's not good to breath it. Good Luck!