First you need to setup the Cart Reader Shield's configuration switches like so:

Doublecheck that the voltage switch is set correctly to 3.3V and that the EEP switch is set to enabled(=towards the back). This connects a 1K pull-up resistor between VCC and the controllers data pin(PH4).

Next plug a N64 controller into the controller plug and insert a Controller Pak into the Controller. Then turn the Cart Reader on.
Navigate to Nintendo 64 and then to Controller. You can use http://rawgit.com/bryc/mempak/master/index.html to manage saved Controller Pak data on your PC.

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Cart Reader V5

Overview
Supported Systems
List of user-created Adapters
Community Discord Server

Build Guide

Recommended Tools
What to order
How to build

More Information

How to order a PCB
How to flash the Arduino
Flashing the snesCIC
Preparing the SD Card
Automatic Voltage Selection
Real‐Time Clock

Advanced

Troubleshooting
Designing your own Adapters
Serial Monitor
Savegame Conversion

Older Revisions

About
Cart Reader V4
Cart Reader V3
Cart Reader V2
Cart Reader V1

Nintendo 64

Read N64 cartridge
Reading a Controller Pak
Reflashing N64 Repros
Reflashing a Gameshark

Super Nintendo

Reading SNES carts
Reflashing NP carts
Reflashing SNES Repros
Reflashing BSX 8M carts

NES and Famicom

Dumping NES Games
Adding auto mapper to a game

Game Boy

Reading a Game Boy rom
Reflashing NP GB Memory carts
Writing custom flashcarts

Game Boy Advance

Reading a GBA save game
Reflashing GBA repros

SEGA

Reading Mega Drive Genesis games
Reading Master System games

Other

WonderSwan (Color)

Flashrom Programmer

Flash-Adapter
AM29F016-AM29F032
MX29F1610
MX29L3211
MX29LV160
MX29LV320
S29GL032