This site has a ton of wonderful bonding articles - I highly recommend reading through them!
Six weeks is probably about average, but it can potentially be a maximum of 8 weeks for hormones (and fertility) to be totally gone in a male after a neuter. Females become sexually mature around 4-6 months of age. At best, you'll have a window of 2-4 weeks between when his hormones are totally gone and when hers could potentially kick in... which could cause dangerous fights. Also, babies will bond with just about anyone but there's no guarantee that a bond involving a juvenile will survive the young one's hormones kicking in.
What I'm getting at is that there's no way you can *fully* bond them and/or safely leave them together unsupervised until after she's been spayed (most vets spay at 4-6 mos depending on the rabbit's size and their own preferences)... and if her hormones kicked in prior to the spay, you'll have to wait a month to resume bonding them (hormones only take up to 4 weeks to dissipate for females).
That
doesn't mean you can't get a jump-start on bonding before then, though! Living in the same room where they can see/smell each other is a great start. If the female can see him when he's running around in the penned area, then it's best to give them equal amounts of either run space (ie divide the run in two) or equal amounts of time in the run (ie alternate who's in there) - rabbits can become jealous when they see that another rabbit clearly has more "territory". Just make sure that, however you have things set up, fighting (or mating) through cage/x-pen bars is not possible.
I would give it at least another week or two for him to get less hormonal and her to get a little bigger (they grow a TON between 8 and 12 weeks of age!), then consider doing bonding sessions. The most important thing is that the sessions need to take place on
neutral territory (ie somewhere that neither rabbit has been before). You also want a fairly small area, both to encourage interaction and to prevent territorial issues... making places like bathrooms and closets good places to start bonding sessions, since they're small and fairly likely to be neutral territory.
*IF* you should reach the point where they feel "bonded" prior to her spay, then it would be perfectly fine to let them out into a run area together as long as someone's going to be in the room who can break up a fight on the off-chance one happens. It's not out of the question to have them live together full time/treat them like a bonded pair in this scenario... but if you choose to do so, you should be aware that there are risks involved
- rabbit fights can be vicious or even deadly
(for what it's worth, I got two girls at 7-8 weeks old and kept them together all the way until their spay date at 5 months old... but I was pretty paranoid about the possibility of hormones kicking in, always looking for signs that fighting had happened (like fur that's been pulled out) and was prepared to have to house them separately at a moment's notice). I honestly wouldn't lock them in a cage together (overnight or w/e) in this situation, just because of the limited space to run/chase/escape a fight
(in my case, the girls had a 28'' x 42'' x 70'' high 3-story NIC condo plus 24/7 access to a "run" that was around 120 square feet - plenty of escape routes and opportunities to get away from each other if someone wanted their space).
If they don't seem truly bonded prior to her spay but she doesn't appear to be hormonal
(or at least, hormones don't appear to be causing problems - if this happens, you'll most likely notice because it feels like you've suddenly taken a BIG step back in the bonding process) then I would keep them 100% separated during her post-spay recovery time (females are usually restricted for about 10 days, though the exact recommendations vary from vet to vet), preferably in a way where they can still see/smell each other, and then as soon as she's off restrictions you can resume bonding sessions... if she gets hormonal, though, then of course you'll need to wait about a month for them to be totally gone before resuming the bonding.
Regarding signs of aggression and such... it's definitely not a totally comprehensive list, but
here's a post I wrote up recently with tips on deciphering body language during initial meet-and-greets between bunnies.
If you'd like a general idea of how bonding might go in the beginning, I actually video-taped an entire hour-long session with my potential trio last week, lol. It was their first REAL session (the three had one meet-and-greet previously that only lasted a few minutes, plus Gaz and Normie had a couple extremely brief encounters before that - basically, I adopted him about a week after he'd been neutered and tested the waters a few times; I didn't do a true bonding session until his hormones seemed mostly gone).
Unless you're just *that* curious (and bored), there's certainly no need to watch the full session!... a few minutes of it would definitely give you a vague idea of how bunnies might react to each other, though, as well as a bit of a feel for positive and negative body language. In particular, Normie (sable coloring/has airplane ears) was positive to the point of exuberant; Nala (Lionhead) was, overall, trepadacious and leaning towards negative in her body language. Gaz (Holland lop) was mostly just a loaf.
[As far as the tone of the session as a whole, I'd rate it as "neutral but appears somewhat promising" despite how disinclined the girls seemed to make a new friend. That may sound counter-intuitive, but when you get right down to it anything short of die-hard aggression is pretty workable if you're patient enough 
.]
[ame]http://www.youtube.com/watch?v=Pfp5CLTx-kE[/ame]
[ame]http://youtu.be/68WmdfQLGSI[/ame]
As for adding a third... that's a whole other can of worms. Trio bonds are more difficult to form and much more volatile overall (ie more prone to randomly breaking down the road). Also, adding a third to an already bonded pair runs the risk of upsetting or even breaking the pair's bond (Gazzles has actually humped Nala during my attempts at trio bonding... and Nala's always been the dominant one in that pair. Fortunately, Nala was too "WTF is up with this new dude" to get upset with Gaz!). Bonding three at once might work and at the very least, you wouldn't have to worry about upsetting an existing pair... however, I'd be wary of trying to add a third to make it easier to bond the first two - it seems like if they can't bond without a third rabbit there then bonding them into a trio may be setting them up for a falling-out down the road. Honestly, if you've never had a bonded pair before, I wouldn't recommend considering a trio right off the bat.
[In regards to what gender would be best if you ever went with a trio, I've pretty much got two answers for that. The first is that I'm a firm believer in personality over gender. That's not to say that gender plays no role at all, simply that the rabbits' personalities can easily trump their genders. Some sources are quick to stress M/F bonds (for pairs) as being best, easiest, whatever; there are even rescues that pretty much insist on M/F pairing and dismiss the viability of same sex bonds. My two happily bonded girls and I beg to differ and I feel their bond is successful primarily because Nala was quick to take charge as the "dominant" one and Gaz was more than willing to be the "submissive" bunny. The second answer is that trio bonding is territory that isn't often charted - even if there *was* a "best" combo of genders, there's not a whole lot of data on trio bonding success rates - from what I've seen, the only viable conclusion is that there's no one right answer. I'm going for a M/F/F trio (which I anticipate succeeding at) and I know of at least two RO members with bonded trios; one is M/M/M and the other is M/M/F.]
Oh, and a side note as far as going without a cage... I'm inclined to recommend keeping one even if you eventually end up free-ranging your bunns. It's nice for them to have a "home base" for their food, water, primary litter box, etc. - something that's strictly "theirs" (and that keeps most of their hay contained in a small area... not that you won't still find a strand or two in your underwear at times, lol). It's also nice to have the cage as an option if you ever needed to lock them up briefly for some reason. My girls have 24/7 access to a huge run area, but they do most of their loafing on the upper levels of their NIC condo - bunnies naturally prefer high ground (in the wild, it gives the best view of approaching predators; in captivity, I suspect they just like looking down on everyone, lol... which is why the highest level of the condo is about shoulder-high to us humans!)
