I'm sorry to have to say this, but alfalfa hay is not good for adult bunnies except in small portions as a treat. It is very rich, high in protein and calcium and should only be fed to growing buns (under 5-6 months) or buns that have been ill and need to regain weight. It's very probable that the alfalfa was the cause of the gas.
Bunnies need grass hay, but it doesn't have to be timothy. There are lots of other types and most are much better for allergic people than timothy. I have orchard and oat hay. There's also horse hay like fescue, rye grass, bermuda grass (coastal). They are all pretty much equal in fiber-content and nutrients and good both for the tummy and the teeth.
Flea saliva is highly irritating. But it's not uncommon for skin scrapings or tape tests to come up clear while the bun still has a parasite, just not in the exact place where the samples were taken. So the Revolution-treatment is really good.
I'm glad you got Revolution, it is a very good, highly effective and bunny-safe anti-parasistic that gets rid of both external (skin-) parasites and internal parasites (worms) - which he isn't showing symptoms of but since he has access to the outdoors, it can be used empirically (empirically meaning without knowing for certain if there are worms) at least once a year.
I hope your bun will get well now, it seems very likely. But get another type of hay. Gas is not harmless in bunnies - if the bunny farts it is harmless, problems arise if the bun can't pass the gas. Make sure he moves around, that's the best way to get a bun to fart =)
Here's a whole chart of different hays and their nutritional values. You'll soon see how very different legume hay (alfalfa, clover) is from grassy hay nutrition-wise.