I use to record each channel (PU1, PU2, Wav, NOI)  separately by soloing them and recording the output. Then I would import them into Ableton and then play each at the same time in ableton after syncing them. Long story short it sonded awful.

How do you guys recommend someone with LSDJ to go about recording, mixing, and mastering?

Experience teaches you what to avoid during the mixing process.  ie: you fuck up enough times and you learn what to avoid the next time around. 

But seriously mastering chiptunes is pretty much the easiest thing ever.  No offensive overtones.  The bass is fundamental frequencies and they SING and never fart out.  The high end never gets into any offensive frequencies.  Now mixing chips with live instruments?  That's a whole other ball game.

From what you are describing ant1, I think you might benefit from trying a mix buss compressor. Compressors can be used in many ways, but mix buss compression means - as you might expect - compressing over the whole mix.

My favourite mix buss compressor is Cytomic's The Glue:

https://cytomic.com/glue

Download the trial version and try it out over your whole mixes.

Staying sort of on topic: compression is the most useful type of effect in the producer's armoury. There are so many ways to use it. I strongly recommend to any aspiring audio engineer that you learn to use one or two compressors really well. Most bundled compressors are fine to learn with, and often sound great too. Learning your compression effects will pay you off in dividends.

http://en.wikipedia.org/wiki/Dynamic_range_compression

Do you ever or often have to scrap whole mixes because of mismatching?

Compare your master with songs you like the sound of.  Do they have sexier bass? Do the highs seem to sparkle compared to yours? Does it sound 'wide'?

Do a lot of split second comparisons and tweak like that. 

Ozone is great, but it literally took me 4 years to really learn how to use it effectively, turns out practice works

To add to Jellica's point, also add in plenty of that frequency that only young people can hear so it annoys them.

just make sure your song is as loud and overcompressed as possible so that its sounds really great on your mobile phone when you want everyone on the bus to hear your tunes.

Do- have many stages of compression

Don't- think your EQs and compressors need to be set the same through the whole song

oh i suck at masters, though ive been practicing.  My usual technique is to throw a master limiter on an auxilary bus before a stereo print track.  Without getting too technical i use the limiter to push up some of the quieter frequencies, make sure the limiter isnt clipping on the in or out and make sure not to over-use it or your dynamics will be vanquished to the x dimension.

edit:  And ive been getting to use the McDSP suites at school.(you were curious about plug-ins, though im no expert the master limiter did add some luster to many of my projects.)

brickwall that shit through izotope. it makes sick drops

Thank you both for clarifying this; it refocused my own use of the word as well as my concept of what mastering is and can be.

Some of my favorite plugins are made by SoundToys

InactiveX is on the money. You master for a medium.

Vinyl mastering for example consists  of a several preventative measures, as well as the standard mastering steps, for the protection of the cutting head (such as ensuring the lower notes are in phase).

Sure, you can do more dramatic changes during the mastering process for "wow" factor and many mastering engineers have made their careers out of having a very distinct aural fingerprint that is represented in their masters. Really though most of the things mentioned (reverb, comp, stereo expansion/widening) can and probably should be done during the mixing stage if you feel it is part of the artistic expression in your work, even if you apply these effects to the entire tune (on the master channel, just to confuse people more).

Feel free to disagree, correct or debate the points I've made. I'd be very quick to suggest that I probably have less experience than most on this board when it comes to this subject. I have however been involved in the mastering process of several releases across multiple genres and the above have been my impressions.

I'm not sure some of you understand quite what mastering is, and how it differs from mixing. It's a common misconception.

http://en.wikipedia.org/wiki/Audio_mastering

Here's the official godinpants trupunx™ mastering suite.