One overall suggestion for these feats before I get to the individual responses: You might want to make everything that scales by HD scale by BAB instead, to make good BAB more meaningful as you said before.

Now, to the individual feats:

Roar of Challenge
[...]
In addition, as a free action once per turn you may roar a challenge at nearby enemies. The range of this ability is 25 ft.+5 ft./2 levels, and you can affect a maximum number of enemies equal to 1+1/2 HD. Any enemy who hears this challenge must suceed on a will save (DC=BAB+Str) or on their next turn they must focus any attacks they make on you.
To simplify this a bit, I'd suggest just making this a cone that affects all enemies in the area, to be more in line with other shout/fear/etc. effects, and scale the area instead of the number of targets (something like 10 feet + 5 feet per 2 points of BAB). That's more for ease of resolution than balance, though, so it's up to you.

Shield Strike
[...]
In addition, any enemy dealt damage by your shield strike must succeed on a Fortitude save (DC=BAB+Str) or be dazed for 1 round. If they fail by 5 or more, they are intead Stunned for 1 round.
Daze is generally a more valuable condition than stun since it's much harder to resist or become immune to it, so it should probably stun on a failed save or daze if it's failed by 5 or more.

Block and Parry
[...]
Yeah, this is a little more complex than I'd like, but its the best thing I've been able to come up with for an active defense.
Here's a possible idea: While someone with Block and Parry is wielding a shield, they may use their Str instead of Dex for AC if it's higher, and when targeted by a melee attack they may expend one attack of opportunity to add half their BAB to their AC against that attack.

Str instead of Dex represents actively pushing attacks away more than dodging, spending AoOs uses an existing resource and integrates better with other feats, and just adding to AC keeps the advantage of AC as a static defense instead of adding more rolls. As it is, BAB+shield bonus is highly unlikely to beat the attack rolls of near-level opposition since you're missing out on weapon enhancements, Str, buffs, and other bonuses, and just rolling opposed attack rolls at will is too time-consuming and swingy, so increasing your existing AC is probably a better route.

Spell Reflect:
[...]
If you suceed, the spell is simply negated. If you suceed by 5 or more, then the spell is reflected back at it's casters, with a maximum range equal to it's original range.
Just as a minor nitpick, you should probably clarify that the total range (distance from caster to fighter * 2) is limited by the spell's range.

You can attempt to negate the affect of AOE spells, though if you suceed the spell still triggers on the surroudning area, except for the space you occupy.
A better phrasing for this would be "If you successfully negate an area spell, it is only negated for you, not for any other creatures in the area. You are not able to reflect area spells back at the caster."

Armor Buster
[...]
Benefit: When you make a charge attack with a two-handed weapon, you can ignore damage reduction on your target in an amount up to 1/2 your BAB. If this value exceeds the amount of DR your target has, then you may ignore any AC bonus from armor (including from natural armor) equal to 1/2 the remaining difference. (or 1 point of AC per 4 points of BAB)
Two things here. First off, fiddling with halves and quarters of things for DR and natural armor isn't all that complicated, but it's more complicated than it needs to be. Ignoring all DR isn't terribly powerful (you can get it with a cheap weapon quality or low-level maneuvers), so you could just make this let them ignore all DR and it would be fine.

Second, two-handed fighting is already pigeonholed into a reckless charger style with the existence of Shock Trooper, so I dislike new feats for 2HF that only function on a charge. In fact, I might make Armor Buster not work on a charge, since that's helpful both thematically (you need to wind up and aim for a weak spot, not swing recklessly) and mechanically (gives chargers something to do when they can't charge), but that's just me.

Putting those together, I'd change the benefit to the following: "While you wield a two-handed weapon, the first attack you make each turn against a target with damage reduction ignores that damage reduction; if you attack a target without damage reduction, you instead ignore an amount of armor and natural armor bonuses to their AC up to 1/4 your BAB." Nice, clean, and effective.

Crippling Strike
[...]
Benefit: Targets dealt damage by your melee attacks lose immunity to ability damage for 1 round.
[...]
This one is probably a little wordy as well. I'm open to suggestions for improvement.
I dislike the idea of disabling immunity to ability damage for a round. Your own attack ignoring immunity, sure, that means you're Just That AwesomeTM, but disabling it this way would seem to encourage the fighter hitting an ability-damage-immune creature so that his caster buddy can shivering touch or ego whip it, and while encouraging teamwork is nice I think that's too abusable.

Here's what I'd do instead: "When you score a critical hit with a two-handed weapon, you may forgo the extra damage from your weapon to instead deal 2 points of ability damage per point of critical multiplier to an ability score of your choice (6 points for a x3 weapon and so forth), aside from Constitution. If your target is normally immune to ability damage, you only deal half that damage."

Reach Weapon Specialist
[...]
I'd like to add something else in conjunction with this feat, but I haven't come up with anything that isn't OP at a low level yet. Let me know if you have ideas.
I don't think you need anything else; this basically turns every reach weapon into a spiked chain, and that should be good enough.

Harrier
[...]
You can affect a maximum number of enemies this way each round equal to 1+1/2 your HD.
You can probably remove that limit; the penalty is easier to track if it just affects everyone within your reach, and in a given battle you'll either be facing a handful of enemies (in which case you wouldn't get the full benefit anyway) or a ton of enemies (in which case you should be able to shine by harrying two dozen mooks).

Lockdown
This feat is essentially Stand Still++, and Stand Still can be taken at level 1, so I'd change the prerequisite to "BAB +6 OR BAB +3 and Stand Still" so it doesn't make someone who picked up Stand Still at 1st level feel like they wasted a slot.

Forceful Leverage
To make this scale and synergize better, I'd just have it let you make a free bull rush attempt against a target you damage without provoking an AoO or requiring you to move with the target, reducing the extra +BAB bonus to +BAB/2. You'll be less guaranteed to move the opponent 5 feet, but if you build for it you can get a pretty high check.