I'm sorry your rabbit experience has gone so wrong. I'm sure that having those males put down was painful for you (and expensive - unless you are doing it the way that the people who are butchering do it, rabbits are rather hard to euthanize).
You have learned (the hard way, unfortunately) several things that I often try to tell people, but which somehow doesn't quite get across a lot of the time. For starters, rabbits fight; particularly bucks. They aren't really social by nature; that's more of a baby rabbit behavior. As adults, they are territorial, even the does. This behavior usually starts at adolescence, which may begin as early as 10 weeks of age. Spaying/neutering helps, but there are a few that never will get along with other rabbits; they are just too dominant. Some rabbits may live together quite happily, but the key seems to be giving them enough space that they can get away from each other when they feel the need to do so. Each rabbit needs to have its special place(s) where it can kick back and chill - boxes and other structures that give them "cover" and get them out of each others' sight seem to make for much happier groups.
Male rabbits (and some females) spray to mark their territory. Some aren't bad about it, but with others, it's like a hobby. Once again, neutering helps, but some territorial marking is just normal rabbit behavior, and some may never be 100% on using a litter box.
Unless you luck onto a rabbit with a naturally friendly, outgoing nature, you will probably have to put a fair amount of time into taming your rabbit. The more handling they get as babies, the more likely they are to respond positively to people, but we are a tall, towering, predatory presence to them until they learn otherwise, and they will run from us. A cage isn't really a bad thing; it provides a relatively small, secure area where calm. positive interaction can take place. People often tell me that they want their rabbit to free-range in their back yard, and I warn them that securing the fence line is only part of the equation. What I usually say is, "if you turn him loose in the yard, you may never get your hands on him again." These are small prey animals, and it seems like everything eats them; they instinctively know that survival depends on detecting and avoiding threats. The incautious rabbit is lunch! If your rabbits won't let you approach them, maybe they will approach you if you sit quietly among them.
Don't beat yourself up about those rabbits that you have had put down. Your sanity is at stake here; some tough choices will have to be made to get your herd thinned down to a manageable level. I just hope you got the males away from the females early enough; some female rabbits can get pregnant when they are as young as 3 months old. We keep pets for the pleasure they give us, not to become slaves to their needs! Hopefully, you can get this situation under control, and start getting some pleasure out of owning these little fuzzy things.
But mentioning needs, why are you giving these rabbits alfalfa? They really do not need that much protein. Some rabbit feeds are alfalfa-based, but they have other ingredients that balance out the protein levels. Some people believe that alfalfa may be harmful to rabbits; some feed manufacturers even make feeds that don't contain alfalfa to accommodate them. If you are giving these rabbits a pelleted feed, you are most likely meeting their needs as far as protein is concerned. They need hay, yes, but it is for the fiber content - most good quality grass hays will do the job, and they are usually much cheaper than alfalfa.
Edited by Bunnylady - 11/2/15 at 8:29am