Wow, this is the kind of stuff that makes me really appreciate it when I get the chance to work directly with a first-time builder... see these aren't really bad things about your choice of airplane, they're almost universal.
Balsa Sizes -- those are virtually never marked. After doing this for a while, your eyeballs calibrate to the nearest 1/16" and you become able to quicly recognize the standard sizes: 1/32, 1/16, 3/32, 1/8, 3/16, and 1/4... 5/16 and 3/8 you don't see much, but they're almost automatic once you recognize the others. When I'm building with similar sizes, I sometimes mark one end of each stick with a highlighter color coded to its size.
Only one side shown on plans -- that's standard drafting procedure and, again, doing more is vitually unheard of. Your method will work, but an easier way with one less chance for error is (for sheet structures) extend marks for the edges of attached parts past the edges of the sheet on the plans, then lay both side pieces over the plans and transfer the markings directly to the edges of the sheets. From there you can open up the two sides book fashion (bottom to bottom or top to top) and pencil the part locations onto the inside of each. (For built-up structures) build the first side over the plan, flat sand that side, then cover with plastic wrap or similar and build the other side directly over the first. Either way, there's no tracing, very little work in transferring measurements, and the sides match exactly.
Separate wings panels that don't match -- that one's a really common problem. It is FAR more expensive to individually plot a set of plans than it is to copy them from a master and, unfortuantely, most copiers have a little error in them -- either they blow things up (or down) by three quarters of a percent (which is over half an inch over the span of a big trainer), or they change the aspect ratio a little, or the paper skids and they curve the lines, or all of the above... and even if none of those things cause problems, your copy is no better than the original hand drawing (believe me, there are some significant errors in the original drawings of some very popular planes). The only way to be sure you don't have a problem is to measure the joining areas for length and squareness before you build.
Control Surface gaps -- yep, that's another one... I've never seen it specified... ever. Again, once you've developed the calibrated eyeball, it'll be a total non-issue. For now, keep them under 1/16" and you're golden, but if you end up with too much, bridging the gap with covering gives an airtight seal that looks good and enhances the plane's performance. Actually, that's true even if your gaps are tight. Allowing enough space for the downward swing should also be a non-issue as long as the leading edge of the control surface has the proper to the upper edge.
So, to summarize, you've got standard blueprints at worst... the problems you've found are even present on very good plans. These are all learning curve items, unless you're lucky enough to find a kit that's so well tuned to the beginning builder that it deals explicitly with these things -- but I've never seen one go to that detail, so if you find one that does, PLEASE let us all know. Meanwhile, looking (in detail) at as many planes as you can will help. And, checking out some of the Harry Higley books offered in the magazines (Master Modeling, Bipes, Mostly Mounting, etc.) should also help speed you up the learning curve. Best, of course, would be to work with a master, but that's often not practical.
BTW, years ago I studied under a master carpenter who taught me two very important things:
- A master is not somebody who never makes a mistake -- he's somebody who knows how to make it look like he never makes a mistake, even after he DOES make one, and
- When you're not sure of what you're about to do, you just have to pretend it's some body else's [house, airplane, or whatever...] and go ahead and do it. (Note: this technique helps you build quickly and confidently regardless of whether the subject is somebody else's plane or your own).