1st: Ability score adjustments. In 3E/3.5E these should always be even-numbered.
2nd: Mohgori. Should be -2 Str, -2 Dex, +2 Con, +2 Int. Bonus versus Giants should specify what it is a bonus to, and of what type (if it's to Armor Class versus Giants, it should specify that it is a dodge bonus to AC versus Giants, for instance, while a bonus on attack rolls against Giants probably doesn't need to be of any named type). Bonus versus magical effects should specify that it is a bonus on saving throws versus magical effects. Elasticity should say simply that the Mohgori have Damage Reduction 5/- against bludgeoning damage, meaning that they suffer 5 less damage from any bludgeoning attack and 5 less damage per round from persistent bludgeoning effects.
Likewise it should say that their Damage Reduction also applies against falling damage as DR 1/-, and that any time a Mohgori would suffer falling damage or the equivalent (such as a Telekinesis spell flinging them against a wall for instance, to use a Core Rules example), the Mohgori may attempt a Reflex save against a DC of 20, and a successful save reduces that falling damage by half instead of applying the Mohgori's inherant Damage Reduction. As a note, remember that being size Small means more than just +1 AC/attack and +4 Hide, it also affects carrying capacities, weapons useable, weight of appropriate clothing/armor/shields/etc., and such. Overall, I think the Mohgori are a bit weak, but neat. I say, give them a free Skill Focus bonus feat, with the caveat that they must apply it to one of the skills they gain a racial bonus with. Also, have Elasticity give them a +2 bonus on Concentration checks and on checks to oppose being bull rushed or tripped, reasoning that their relatively soft body, hardy constitution, and keen mind render them less prone to distractions, while their rotundity, softness, and lack of legs makes them somewhat more stable than other folks.
3rd: Cogs. Ability score adjustments should be '+4 to one ability or +2 to two abilities, chosen at creation, and either -4 to one different ability or -2 to two different abilities, chosen at creation'. More balancing would be to specify what ability score adjustment combinations are acceptable, since all ability scores are not balanced. Str and Dex are strongest, Con and Int are close second, while Wis and Cha are somewhat weaker. So maybe 'Cogs choose one of the following combinations of ability score adjustments at character creation: +4 Str, -4 Dex (ooc: hulking but not as tough as its bulk would indicate, made with more rickety but powerful and bulky components); +4 Str, -2 Int, -2 Wis, -2 Cha (ooc: made for brutish tasks and given subpar mental components within the small spaces not taken up by powerful servo-motors or whatever); +4 Dex, -4 Str (ooc: made with many agile joints and fast-reacting gears/pneumatics/hydraulics, as well as precision motor-reflex joints and manipulators, but not particularly powerful and not made to hold up under the strain of heavy loads); +4 Dex, -2 Str, -2 Int (ooc: like the previous one, but more decent motor power, and a compact frame that has little room for mental components); +4 Int, -4 Wis (ooc: very intelligent and quick to learn, but with quirky/falty reasoning and poor sensory components); +4 Int, -2 Str, -2 Cha (ooc: calculating and quick-learning, but somewhat detached and cold personality-wise, with some bulky mental components taking up space where minor motor-units might be); +4 Wis, -4 Cha (ooc: even more detached and introspective, philosophical but out of touch with people, rational but insensitive); +4 Wis, -2 Dex, -2 Cha (ooc: inflexible in mind and body, but very rational and observant, steadfast but stubborn); +4 Cha, -2 Str (ooc: impressive design and social faculties, but a slim, sleek frame that is somewhat lacking in power, though not particularly frail); +4 Cha, -2 Dex (ooc: likewise, but less sleek and more decorative, with some slow-moving/reacting internal components); etc.
Anyway, for Cogs, the low-light vision seeing only black and white is odd, and should just work as per low-light vision in the Player's Handbook for 3E/3.5E. The skill bonuses and initiative/flat-footed benefits are fine, and balance out the lack of a human's bonus feat and bonus skill points more or less. However, remember that being Constructs makes Cogs immune to many things, not just necromantic stuff and positive-energy healing. They become immune to critical hits and such as well, for instance, as well as a variety of other things. So specify in the Cog's Construct definition what normal Construct traits they lack, if any. Merely being a Construct without a Constitution score, however, practically qualifies them for a +1 Level Adjustment / Effective Character Level by itself. It makes them immune to anything requiring a Fortitude save unless it affects objects, for one thing. As for Metallic Body, only objects have hardness, creatures (including constructs) have Damage Reduction instead where applicable. Do not make them roll for DR and Natural Armor, it's unfair and imbalanced. Give them a straight DR 3/- that applies against all damaging effects, and a +4 natural armor bonus to AC. As for armor costs, say that Light and Medium armors cost double, while Heavy armors cost triple (except full plate, which should only cost double because it's normal cost already factors in some form-fitting). The DR and natural armor, combined, should result in the Cog having another +1 LA/ECL, for a total LA/ECL of +2.
As for a Cog's Modifications, you didn't mention in the document how many slots they have or what they can be used for specifically, so there's no way to judge the potency/usefulness of that capability. The only thing you mention is the 'Flotation' modification, mentioned in Metallic Body's no-swimming bit. For that, note in the description that the -6 Swim penalty replaces the inability to swim. The Forge-Built feature seems rather odd. It gives them an odd and potent replacement for natural healing (you don't specify how it works though, like saying that the 'points' are hit points that it heals, specifically). Also, you make Mending and Make Whole into rather powerful healing that is easily available (far as I know; you make Mending, a 0-level spell, repair Cogs as if it were a 1st-level Cure Light Wounds, for instance). Only weakness there is that the Heal spell doesn't help them, and there are no Repair spell equivalents to that, but it only matters at high level anyway. For HPs healed through metalworking/clockworks skills, you should note that it's 1 hour of work and 10 GP per 5 hit points rounded up. You also need to make the Rust description more specific. Overall, I figure the Cogs are a strong +2 LA/ECL race given their traits, or +3 LA/ECL if you specify that they have all proper Construct traits (not just the immunity to necromancy and lack of Constitution that you note). And yes, this is after taking into account their meager limitations against swimming, water exposure, and most magical healing spells, and even considering their restriction against using magic. My LA/ECL assessment is actually more than fair considering their many strengths/immunities, resilience, and capacity to choose their ability score adjustments.
4th: Bahabi. Ability score adjustments should be +2 Con, +2 Wis, -2 Int, -2 Cha. Skilled Herbalist should grant +2 Heal and Profession (Herbalist) in my opinion. The Bahabi's bite attack is unclear and needs to be reworded in accordance with the natural weapons of Monster Manual critters and such. Given their scent abilities, natural bite attack, and such, despite their few penalties, I would give the Bahabi a +1 LA/ECL, though they'd be a bit weak for a +1 LA/ECL race, but they're somewhat too advantaged for no LA/ECL. You mention them being good marksmen, maybe give them +2 Dex or +2 on ranged attack rolls to reflect that and make them a good +1 LA/ECL race.
5th: Vallen. Given that your ability adjustments seem to be based on 2E or earlier D&D/AD&D thinking, fix the Vallen ability adjustments to +4 Wis, -4 Con. You don't specify their flight maneuverability (described in Monster Manual), and mind you, speeds in 3E are not per round but rather per move-action or partial action (two move actions or a move action and a partial action constitute a full round). Flight is an instant +1 LA/ECL for a race, as it is a powerful and versatile ability (even a flight speed of 5 feet would be far more useful than an infinite bonus on Climb/Jump/Balance checks, really). Low-light vision should be fixed to give full-color sight, as per the Player's Handbook, otherwise it is pointless for a race with Darkvision. The beak natural attack must be clarified and fixed as per 3E/3.5E Monster Manual stuff. Fragility should apply with falling damage as well as bludgeoning damage. Dive bomb should be clarified. Overall, with their extreme visual acuity (they're the ultimate snipers, and airborne to boot) and flight capacity, they should have a +2 LA/ECL at the very least, maybe a +3 depending on what flight maneuverability and other racial traits you give them.
Alright, it's 3 am in Arizona now and I realize I shouldn't have bothered starting on this reply at 1 am.....didn't expect to take so long going over it. Sigh. Sleep now, think later. Down with insomnia!
