How are you planning on putting your cards in any digital format? It's going to be a lot of manual entry no matter how you slice it. Zorbec's is the only other deckbuilder of note, and I'm not seeing a way to restrict the overall card pool.
Buying up the cards in the merchant is going to be a massive hassle though, especially since in most browsers you'll have to make twice as many clicks for some reason. The idea that comes to my mind is to add all your cards to the deckbuilder and save it as a deck, perhaps divided by block or culture. Then you can browse your cards in a meaningful way. Perhaps open a second window and build your deck up from there, or pare down from the full collection. Open up your Fellowship and Towers master lists to see what your Towers Standard options are. Just be careful not to save over your list! If you end up doing this, I might consider making an extra copy of each of them as a backup.
The next best alternative, in my thinking, would be to use the Excel version of the wiki database and go down the line marking your quantities of each card. Then you can use Excel's filters to see your Shire cards from a certain range of sets. This would be the easiest option for you to set up, but probably the most difficult to do anything with.