Hi there,
Also wanted to provide support/encouragement for your project. Having done multiple single instrument arrangements of VGM I can understand the huge challenge and effort required. They are among the most tricky type of music arrangements I make, both in terms of timing, tuning and execution. It's also great seeing my instrument's(violin) sibling trying something similar =)
Calum provided some excellent feedback.
Apart from the tuning (especially with the octave section) and some timing issues there were 4 other things I wanted to add.
1. At 14 seconds in or so you can hear where you have cut the previous track quite noticeably, using fade in/fade out if you wanted to cut tracks might help in Audacity.
2. There were a few sections where the file sounded clipped, heard more in the cello track panned left.
3. The other thing that has been picked up is the sound quality and use of reverb. I would strongly suggest using a DAW/VSTs to add reverb - or to record in a room that provides natural reverb.
4. I would suggest some mixing to allow a specific part to stand out and to direct the listeners ear to where you want it.
The gear used for violin and cello is of course different but maybe mine will help:
Gear I use-
Microphone: ATM 350 Condenser microphone (~$330 AUD)
External Soundcard: MobilePre USB ~2nd hand (<100 AUD)
Recording Software: Audacity (Free!!!)
DAW: Fruity Loops (also use this to add reverb and mix)
And then a lot of video gear/programs, but you won't be needing this added expense =)
So with your goal you should be able to create some really good quality recordings I think!
Some of my multi track stuff I make for YT, if you want to hear the quality of the gear:
OoT: http://tindeck.com/listen/nsel
Pokemon: http://tindeck.com/listen/vvko
Portal 2: http://tindeck.com/listen/pfic
Anyway, hope this helps - and I hope your project goes well! People here are very knowledgeable and friendly to boot - so don't be shy asking for advice/feedback!