Boriz, thanks for the ESR tip.
Experimentation is a great way to learn. Especially with switchers. You will soon discover how useless spice is when it comes to modelling DC-DC converters unless you include models of your layout and EMI patterns.
Only building a few and doing thorough tests will make it sink in.
Don't forget, building it on breadboard WON'T give the same results as a properly layed out board. Winding your own magnetics is a great idea. If you are going to try to get them small by going up in frequency, don't forget to try bi and tri-filer windings. It can really help with keeping down R due to skin effect. Far less "PCB real estate" than multiple low ESR caps.
You WILL need to brush up on your maths if you ever want to get ultra high efficiency within the next few years. Snubber networks and compensation feedback can't be experimented without a LOT of time. It would be quicker to learn and understand the principles than it would be to grope around in the dark trying things out. You'll also need a very good 'scope.
The first thing to get rid of is the diode. This requires getting your timing right or you will get shoot-through which does not need to be more than 100nS or more to lose everything you gain. Not to mention popping the FETs if it's much bigger. Oh yes, get the snubber wrong and the FETs go in uS.
There's a lot of info available on the NET to help you in THEORY, but you simply can't beat practice to find out what it's like for real.
I wish you all the best.
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Could I use an LDR to move the controllers peak-efficiency-point around according to conditions"
That's NOT the way to do it.
Monitor the power in/out and adjust accordingly. That's the whole point of MPPT. (I'm not sure you've got this yet!)
"
a swap-out facility for the main components"
After you've built one, let us know how that idea went.
(don't forget to model the "extra cap/inductor lengths in your spice model).
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How does frequency and duty-cycle relate to input load and output power"
It doesn't. But then you knew that from your spice model didn't you
Please let us know how it all goes. Switchers can easily become a lifetimes work.
EDIT:-
If you find Dippy's link a little too much. Here is the BASIC version.
http://www.powerdesigners.com/InfoWeb/design_center/articles/DC-DC/converter.shtm
Like Dippy, I don't understand your desire for SEPIC. However, if you want to learn about switchers, a FULL understanding of the SEPIC topology will go a long way.
(you'll also understand my comment about low ESR caps vs low R inductors)