TheBudReaper: Here's my two cents worth:
1. I haven't had a problem with air stones clogging and I've found that the 5 gallon aquarium pump from Wal-Mart does very well in a single A/G. I've tried a variety of stones: a ten inch which I could hardly fit into the reservoir, a 5 inch which was still a tight fit and the best so far has been is a two inch round stone that I got from the 99 cents store in the pet supplies department. It comes in a pack of three for 99 cents. If you run two A/G's you might consider the ten gallon pump aa a five gallon pump won't handle them both.
2. As far as lighting is concerned, I think a lot of people don't know how to use the lighting A/G gave them. If you have an old style seven holes model with a short 12 inch arm/light stand and a two lamp hood then in my experience that's a stretch for growing M/J. If you upgrade to a three lamp hood with a 24 inch arm/light stand and you use reflectors you can get buds all the way down to the planting deck.
I have friends who have done like you said and removed the hood and rigged an assortment of lights, they pay a heart stopping electric bill every month and they haven't done any better than me. If you have a 'Space Saver,' A/G-6 or an A/G-3 then I think you have an uphill battle ahead as those are the least applicable to what we're growing.
I used to use mirrors to send the light back up to the the normally shaded lower portions of my plants until I dropped one and it shattered into a million pieces. Now, thanks to a suggestion from someone here in the forum, I have 2mm Mylar glued to recessed florescent fixture lenses I cut down to size and they're light a s a feather and a whole lot safer.
A lot of people do make some radical changes in their A/G's but I can't really understand why. You have a complete, compact growing system that's very economical to operate and right away they start complicating it. Then why use an Aerogarden? Why not a bubble tub? that's just a bigger more complicated version of the A/G. What Cervantes said in his book is so true, "Stoners seem to complicate everything." Granted our A/G's weren't designed to grow M/J, but with a very minimal amount of modification they can. My best advice is: If it ain't broke don't fix it.