I will start by saying I have not reviewed your project. But with that said I have to agree with Peter in the use of a prebuilt MCU module. You could use an Arduino Pro mini 3.3v if you don't need USB for anything other than programming. You could use a Nano 5v as Peter mentioned if you need USB all the time. Or you could use a new Arduino Pro Micro 3.3v which is based on an Arduino Leonardo and has built in USB like the Nano but has the same small footprint as the Pro Mini. The pro mini can be purchased for $2 each with shipping if you can wait many months or a little more for decent shipping. The Pro Micro and Nano are both about the same price and not much more than the pro mini.
I would also suggest something like a ESP8266 if you only need a few pins as it is 3.3v which you want, Arduino IDE compatible and has built in Wifi (limited memory though). If you need more pins you could also use an ESP32 which has bluetooth and Wifi plus tons of GPIO's and is also 3.3v and Arduino IDE compatible. The Esp8266 is really low cost and the ESP32 is also a good price (under $6 from a few places even in the US), The draw back with the ESP modules is no built in USB but you do have Wifi and Bluetooth so no real need for USB.