Glad it's worked out so far! In the end, no matter how much tinkering you do these are just starter decks. Not only were they created to showcase common functions (archery, fierce, damage) without being too complicated (no conditions or maneuver phase actions, for example), they were created to allow easy avenues for improvement (other than skirmish events both decks have a lot of needs), and the Free Peoples were created to handle the sorts of threats that low-budget Shadow sides could put out (hence all the skirmish events). It sounds as if they've done their job as starter decks and since you've got a solid collection going, it's time to move past what they are and figure out what they're going to be.
Nobody is born with deck balancing experience. Instead you gain some every time a deck you build loses (and occasionally when it wins). You've got at least 6 games of experience with these two, hundreds of cards at your disposal, and at least 11 cards to add to each deck. Neither of them are anywhere close to fully designed, so there's no reason to "hold back" and keep your strongest cards out for the sake of balance. Determine a need that your deck has, flip through your collection to see what can meet it. You found that the Theoden deck is vulnerable to swarms, for example. This was caused by an inability to get companions on the board, so maybe put more companions in the deck. If/when that then causes pain in other ways (
Death to the Strawheads easily overwhelming important companions, for example), look for Frodo support such as
Severed His Bonds or ways to take minions out before they can be assigned such as
Rohirrim Bow.
If you want to bring them to Gemp exclusively to play with the same opponents you would face in person, I think you'd do best to stick to your collection. At least at first. That way there's no disconnect between what happens online and what happens in person, and then both of you can evolve your decks together. If you want to play them against random opponents though, I think you'll be better off starting from scratch. There are so many weaknesses built in that it'll be hard to know where to start and once you finish the decks will look pretty different from how they look now anyway.