You made a wise choice to build a Lightning Rod. You have a couple choices on how to keep it powered.
Rainmaker's work, but typically only produce rain and not a storm, so you'll need to pump out iron fences and place that sucker at about Y 5 to get enough power for it that way(which, in theory, with iron fences up to the current build height, could produce power during clear weather as well)
A better choice(assuming you use MystCraft and have the needed symbols) is to use it on a eternal storm world of some kind. Technically you need to use IDSU's for this build, but in realty, you can just set up the Matter Fabricator and the Lightning Rod in the age, and pump the scrap in and UUM out with some kind of trans-dimensional transport device.(aka either a couple Ender Chests or some Item Tesseracts)
A horribly expensive option(that totally would work, though) would be to use a Trans-Dimensional Transport Device to send a Gravichest Piece to a MFSU on the storm world, and then back to a MFSU in your base, and use the MFSU to power the Matter Fabricator. The Gravichest Piece can be fully charged or drained in ten seconds and holds a lot of power(basically a MFSU IIRC), meaning you can fully charge a local MFSU with power from a offsite MFSU in twenty seconds.(excluding time needed to transport the bloody thing)
But I fully Suggest the Rainmaker and a lot of iron fences, because it can be done without MystCraft.(which means it can be done quicker and likely with less lag from having a new dimension loaded)