I don't think you will like this because I doubt it could be done at home. It does have a lot of advantages so I will mention. Several FPGAs (field programmable gate arrays) are coming with source for a on board microprocessor. What this means is that each pin can be configured for what you want (and there are a lot of pins). And you don't have to buy a processor it can be programmed in. Altera makes the cyclone which is where my company is headed.
If you want more info I will help you find it. I don't think you will want to go this way, but I figured I should al least mention is an option.
I've done a fair bit with FPGA's, and it's a world away from the current level of project you're considering, IMHO. Yes, you can get FPGAs with embedded systems, but (a) they're expensive, (b) they're unfamiliar, (c) they're hideously complex by comparison, (d) they're not available in home-friendly soldering packages, (e) interfacing them is more awkward, and (f) you have to start worrying about parasitic capacitance, trace load and impedance, matching traces on the PCB that run at high frequency, spread spectrum clocks etc. etc.
I tend to use BGA chips, which solder reasonably well in an SMD oven at home, but not everyone has an oven, and the PQFP devices are normally very fine pitch - 0.5mm is typical.
If you're into coding C, a verilog module is superficially similar - indeed I used that argument when I was pitching an internal project. The problem is one of "coding" - you have to wrap your head around the fact that almost *everything* happens in parallel due to the 'always @ (sensitivity-list)' statements. It's a different mind-set, and it takes software programmers a while to adapt, at least in my experience.
You *can* do FPGA's at home (I do), but it takes a reasonably sophisticated setup - I use the PCB machine to engrave the circuits, a solder-paste dispenser to put the solder-paste on the circuit, and an SMD oven to actually solder the parts. It's do-able, but it needs a level of investment that I don't think is typical. Bottom line: I would stay away for something like this, but hey, don't let me stop you if you're keen
Simon