1) I've never had an acoustic with a real mechanism to adjust intonation, but you can compensate with technique. For instance, most of the guitar solo parts in your song sound fine, but at certain times when you hold certain notes, they sound really flat (going from memory here). Instead of just hitting a note and holding it, put a little vibrato into it which will mask the flatness and make the note sound more pleasing. If it's an open string, avoid using it and play the part in a different position if possible.
2) You say you didn't add any reverb...well I seem to remember the drums sounding like they had a lot of reverb on them. I can't remember but I'm pretty sure they were sampled, right?. Try finding samples that are much more dry. Using wet samples is almost impossible because you have to create the rest of your mix around them. You can find a couple good acoustic dry samples at
http://www.2dcd.com under the sample sounds section. Snag ALL the samples they put up, they're great! As far as EQ and compression...avoid compressing sampled drums as it's only necessary in certain situations because the samples always play at the same volume. You can EQ a little bit but there are no "EQ settings" that can be recommended. You just don't want your snare & kick fighting with other instruments. I didn't hear any bass, so the kick should behave. For the snare I've found that using a real snappy sample (there's one at 2dcd) to start with is the best bet.
3) How did you record the electric guitar? If you're getting a lot of reverberation from your room then try close mic'ing it and adding fake reverb in the mix (if necessary). Reverb is like the glue that holds everything together...it's hard for an amature like me to explain and it's even harder to use effectively. Start paying attention to how things sound in various rooms as you wander about....that's what reverb processors are for; putting your instrument into the room of your choice (too bad it's not that simple).
At any rate, I wouldn't worry about reverb, EQ, or compression at this point. The mix with the drums was really off just in basic track levels. In most cases you should try to get as big a clean mix with your raw tracks as you can so that you can get a better understanding of what exactly needs to be done. Don't just grasp at straws looking for "recommended compression settings" and the like. Hear what you want the mix to sound like in your head, and then try to duplicate it using the tools at your disposal. Don't worry if you can't seem to get it right. I sure as hell have never gotten anything right. The good news is that once you start learning these things you can come back with specific questions and get specific answers.
Slackmaster 2000