aarondc:
The Mega has more inputs than I have had hot breakfasts, and I am using uh 6 of them. :~I got the Mega because it had 256k of flash. I didn't want anything getting in the way of my C programming, and that was the most memory in any of the units. The sketch running currently weighs 12kb.
Ouch ... 
You'd be surprised how much you can fit inside of 32K.
aarondc:
Have you designed a custom board yourself?
Is Eagle good enough?
Plenty, and more than just "good enough".
aarondc:
I am really keen to make it SMD so have been watching reflow videos with ovens and heat guns. Am very excitement about the possibilities.
My very first board had SMD parts on it ... I didn't bother doing any practice soldering, I just jumped in. Other than one miscalculation with a regulator (which was solved by cutting the trace and soldering a jumper wire.) Since then I've done several others, both for myself, as well as for others (paid.)
I don't use neither an oven nor a heat gun. I use the skillet method.