The chops you're referring to around 2:40 sound like some of the default Grossbeat effects, or at least wouldn't be any more complicated than that would be. 

Just don't listen to the entire 'set' of bars on repeat while you tweak the sound.  Say you have an 8 bar section and you're changing the tone of a single synth in subtle ways.  Solo the synth while you tweak it, checking often (but not constantly) against the whole track.  Or rather than even looping the soloed synth, just tweak it while playing your midi keyboard, and check the actual melody and context of it after you settle on what you think the change should be.  You want to lessen the amount of time your brain is just hearing the exact same thing over and over again, so just break it up!

I mean, look at it this way:  Would you ever say "I don't need to know anything about how a compressor works... I just use my ears and that's good enough for me!"?

Sure, you COULD say this, and use a compressor and still make things that sound okay.. but you won't actually even know what you're doing besides "this knob makes it quieter somehow; this knob makes it punchier".  Knowing *what* the threshold actually is, *what* the ratio is, etc is so valuable in helping you *use* a compressor!  Basically, knowing what you're doing will only help you to use what tools you have available.

The trap of "music theory will restrict me" CAN be true, but only if that's your starting point and you become afraid to explore and branch out.  If you're taught that I - IV - V - vi is a chord progression from the start, you will not understand how you can deviate from that.  If you're already used to exploring and messing around, it can't hurt to learn what a I - IV - V - vi progression is so you can start to identify its use.

MarrowMachines said it best (or at least, resonated the most with my experiences).  Essentially you are going to be staring at a giant puzzle, where many parts connect to many other parts, and you're going to need knowledge of all of it before you really feel comfortable creating music: 

How can you write a song if you don't know how to use your DAW?  Or know some theory, at least enough to get started?
How can you start using your DAW if you don't know how the plugins work? 
How can you know how the plugins work if you don't know what the functions they're performing accomplish? 
How can you learn about the various functions without knowing what's out there, and why you'd want to use them?

The list goes on, and I didn't even touch on things like programming drum patterns (a genre-specific web of knowledge of its own) or sound design and synthesis.

The main takeaway though is *don't get discouraged*.  Over time, as you absorb more and more information, even more information will become just a little bit more accessible to you.  The trick is to wade in there and accept that you will feel lost.  Don't give up.  Google everything you don't understand. Look at the manuals for plugins/DAWs to get the explanation for how things work, and then google those things again when you inevitably don't understand.  Get used to hunting for tutorials, articles and videos to explain concepts, and searching for even more to clarify the parts of those that elude you.

Eventually it starts to come together.  I've been doing this for 3 months now, just as a hobby outside of my fulltime job, probably averaging less than an hour a day to be honest.  I've already reached a pretty solid understanding of a whole variety of topics just from eagerly consuming every bit of information I can find.

Good luck!

http://www.amazon.com/How-Make-Noise-Frequency-Modulation-ebook/dp/B008H7CEQG

I highly recommend buying this book to understand some of the basics about FM synthesis. It's a great way to understand how deep the modulation and parameters you can shape to have a really dynamic sound. It's only like $3.

I also hope I don't get kicked off the forum for really liking this book.

I found this online: http://www.pirot.org/phpmyboard/uploads/c7/f5/Simon_Cann_-_How_To_Make_A_Noise.pdf

Not sure what's legal or not, if this was a free version released by the author or what... but it does contain a wealth of information.   Ond something I've never seen before: someone going systematically through combinations of all the major waves and how they sound together.  Check out around page 26, and 56.  Crazy amounts of detail on all sorts of combinations.  An interesting approach..

^ Not sure what you mean.  The directions are the same.  It's a detuned saw, put a low pass filter on it and decay it with an envelope to make it plucky.  Follow his steps for detune and volume balance and you're done, no?

I'm still a noob so maybe this isn't the best way, but I would start by linking a peak controller with an EQ to duck the appropriate frequencies of the sound.  Then you won't have to worry about your split audio sounding different from your original when recombined.