Hi Mark,
I know I run the risk of being tared and feathered for saying this on this "painters" forum, but: "I love Monokote" ;-) I am far from being an expert, but after using it for the past 37 years, I have learned a few things about how it behaves. Or in this case: how it misbehaves!
Most people still think that it is the Monokote that is moving around, stretching, and contracting and causing the wrinkles we all hate. It does move a little, but the real problem is with our wood! It absorbs enough moisture to enlarge just enough to cause our problems when it contracts again.
We usually build inside where the wood is relatively full of moisture and the whole plane is just a little bit larger than it will be when we take it out into the sun where it will dry the wood making the whole plane shrink just a little bit. This leaves the Monokote loose, with those ugly wrinkles.
The solution is to get your plane out in the sun on a warm, perferably dry, day. Leave it there until it wrinkles. Then use your heat gun, and/or iron with a sock, to shrink the Monokote to conform to your now "slightly smaller" plane. I'm so fanatical about it that I run an extension outside so I can shrink it in the sun!
I do this with ALL my planes. RC and CL. Sometimes it takes doing it a few times, but then it is wrinkle free FOREVER! I have an Olympic II sailplane that is now 30 years old, and the MonoKote is still tight as a drum, even in the sun. I also have a 30+ year old "TF Combat Streak" that flys as both an RC plane and a CL plane that is also wrinkle free.
Now you can begin to see why our ARFs come with some wrinkles. My guess is that they leave the factory in "humid" China, (across a wet ocean,) with PERFECT Monokote jobs. You can imagine how good those people are after covering their "1,000 th" plane! ;-)
Of course, it goes without saying, that all the other suggestions you hear are helpful. Good wood prep, smooth, and dust free, will help. Also, when you use the heat gun, it really helps to use the Monokote mitten to press down on the film, while it is hot, to ensure it sticks to the wood.
I hope this helps with your problem. Please let us know how it all comes out.