I would also love if AudioInjector made a card with "instrument" inputs. The Pro and Isolated cards are great, but the physical footprint is just too large for stomp boxes IMO.
I hit the issues you list in developing my project, pi-Stomp (
treefallsound.com). Yes, the pi 5v power rail is quite noisy, but I was able to tame it enough using a LDO regulator (
AMS1117-3.3 same as the Zero card uses) and a 10uF oscon cap on the output side. Having a separate analog ground (for your buffer preamp and its regulator) from your digital ground (pi and everything attached) helps a ton too. The AudioInjector card is the single place where my grounds are connected.
Starting with a rather clean power supply helps too. The one I supply with all of my kits has 1% line regulation, 4% load regulation and 50mVp-p ripple. If the supply manufacturer doesn't list their regulation specs, you can guess it's pretty noisy.
Once I had clean power, the next challenge was maintaining headroom. Even a LDO reduces 5 to 3.3, so you'll want a rail-to-rail opamp. I tried 6 dual opamps and settled on the MCP6292 due to its noise performance (speced, heard and measured). I configure it as just a simple non-inverting buffer. Same as the second to last circuit here http://www.muzique.com/lab/buffers.htm but with 2M resistors to yield 1M input impedance. You could easily configure it with some gain as well by adding a feedback resistor.
I've also dealt with adding MIDI (DIN and USB). USB you get for free via the pi USB connector. DIN MIDI just requires an opto isolator, a few resistors and a diode. If ya wanna chat about any of that, let me know.
Cheers,
Randall