Your pricing of the small masterwork light repeating crossbow is correct.
Your pricing of the continuous master’s touch is correct per the guidelines. As a DM, I might not be so sure I like that price, however.
Your pricing of the at-will use-activated magic missile is correct. However, it would not fire missiles that deal 3d4+1 damage, as you seem to imply. It would instead fire three separate missiles that deal 1d4+1 damage each.
You have a mistake when you add them together: firstly, you dropped the \$\times2\$ multiplier from the duration note on master’s touch: it should be \$10,000\text{ gp}+4000\text{ gp}\$, not \$+2000\text{ gp}\$. Moreover, you missed this note:
Multiple Different Abilities
Abilities such as an attack roll bonus or saving throw bonus and a spell-like function are not similar, and their values are simply added together to determine the cost. For items that do take up a space on a character’s body each additional power not only has no discount but instead has a 50% increase in price.
For one weapon with two different effects, you need to pay half-again the cost of the continuous master’s touch. So the cost should be \$10,000\text{ gp} + \left(4000\text{ gp} \times 1.5\right) = 16,000\text{ gp}\$.
Finally, Eberron Campaign Setting has a page (268, to be precise) on warforged components. It includes statements like
A warforged component usually occupies the same space on the body that a magic item of the same kind normally would.
Likewise, armbow specifies that it
attaches to the arm of a warforged, completely covering the hand.
So assuming that this item uses up your character’s hand like the armbow does, it should cost \$16,000\text{ gp}\$. If it does not,
Components that do not occupy any space on the body cost twice what they would cost as ordinary magic items.
Thus that would be \$16,000\text{ gp} \times 2 = 32,000\text{ gp}\$.
Either way, the fact that the base cost is less than the price of the armbow, despite having significant extra features, suggests to me that your DM may very well dispute these prices. I would.
A magic weapon must have a +1 bonus on it before receiving any other special weapon properties. But you aren’t enhancing this as a weapon, you are treating it like a wondrous item. The rules don’t really cover this possibility; I would probably require the +1. But a +1 is all you need; after that, you’re free to put as much other magic on there as you want without needing a higher enhancement bonus (with the exception of the more powerful weapon augment crystals).
Any enhancement bonus on the item would add to attack and damage, yes.
For costing these, the fact that you’re adding features to a magic weapon means that you need to consider that 50% premium again. You have a \$10,000\text{ gp}\$ component (the magic missiles), a \$4000\text{ gp}\$ component (the master’s touch), and a \$2000\text{ gp}\$ component (the enhancement bonus, assuming you go with the minimum +1). The second and third each cost 50% extra because you’re combining them on one item. Like so:
$$ 10,000\text{ gp} + \left(4000\text{ gp} \times 1.5\right) + \left(2000\text{ gp} \times 1.5\right) = 19,000\text{ gp} $$
This adds onto the \$550\text{ gp}\$ cost of the base item, so your total is \$19,550\text{ gp}\$. Again, twice that if it’s not taking up your hand.
Best Answer
Probably the most useful spell for your purposes is the 4th-level sorcerer-only spell wings of flurry [evoc] (Races of the Dragon 119) that is considered by some broken because of its uncapped damage and its ability to hit a great many targets at once. Another factor may be that the spell also dazes those who fail the Reflex saving throw against it. It's a nasty spell.
Also of interest may be the 3rd-level cleric spell venomfire [trans] (Serpent Kingdoms 158) that's one of the game's nastiest spells, and by my estimate routinely house-ruled to be more reasonable or banned outright. The spell causes the subject's "venom to become caustic, dealing an additional 1d6 points of acid damage per caster level with each use," therefore enabling some creatures to deal damage with it multiple times per turn. Exploiting the spell's effect becomes a matter of finding a way to poison one's attacks, like by using the collar of venom (Book of Vile Darkness 114) (50,000 gp; 3 lbs.). (Also see this answer on "Use feats to spit in a 15-ft. cone an injury poison that's linked to a poisonous bite.")