Applied Unification is a KubeJS script that should be able to be used just by dropping the script in the server_scripts folder, like described below. It makes all items in both mods convertible both ways, so if you get a Refined Storage item from a quest you can convert it to an Applied Energistics 2 item. The same goes the other way, if you need a Refined Storage item for a quest, you can make the Applied Energetics 2 equivilant then convert it to a Refined Storage item (and convert it back again, of course).

It is configurable, just open the .js file in the text editor of your choice and change the options at the top. These include:

Disabling either way of the above conversion, or both ways.
Polymorph support, for the rare cases an item has more than one equivalent
Removal of all base Refined Storage recipes, and a whitelist for ones to not remove. (Will not remove some modpacks custom recipes, this is due to a limitation with KubeJS) This is on by default so you are less tempted to use easier Refined Storage recipes and convert them to Applied Energistics 2 items immediately.
Options to make core Applied Energistics 2 resources craftable from common resources, for when you are adding this to a pre-generated world or playing a skyblock.
Gating of the inscriber behind key Refined Storage components so there is no getting advanced storage before the pack creator intends.

REQUIRES:

Applied Energistics
KubeJS (this is already in most modpacks)
You can also add Polymorph to provide some extra functionality.

TO USE: Unzip then drop the AppliedUnification file into the server_scripts folder inside the kubejs folder of the modpack. A reboot of the pack is not required, merely running /reload should load the script. NOTE: AE2 will require a reboot upon adding to the mods folder.

$Screenshot showing that the file path should be: <modpack>\kubejs\server_scripts\AppliedUnification.js$

Any modpacks this does not completely work with please report in the comments, I will do my best to fix it. Can be used on servers, however the clients will need to have Applied Energistics 2 installed, but will not need the script. Tested with Enigmatica 6, Loafcraft: Sourdough, Seaopolis.