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I'm trying to create a custom NFC reader/writer. I've been able to use a linux machine with Eclipse to write a java program (and daemon) that controls a reader writer like an ACR122U. So basically on shutdown and startup, it can read nfc data and then transmit it. But now I want to downsize this. I want to put breadboard together a device that is way smaller (palm of your hand) that reads an NFC tag/phone and transmits it back through a serial port (I'm assuming that's easiest). I understand I need a microcontroller and a PN5XX chip. I'm thinking I need a flash rom to put the instructions on. Does anyone know how I could get started creating this?

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You could start by using an Arduino paired with this shield to interface with NFC tags. The Arduino is capable of communicating with the PC over USB.

Once you have a prototype built with the Arduino and NFC breakout board you could buy all the required components in miniature discreet form.