If you compare your clr2 spell to sound burst (the cleric's first offensive 2nd level spell that I can recall) you will see that yours is way too powerful. A 3rd level caster casts sound burst and does 1d8 damage to a small radius. Your spell does 1d6+1 to 2 targets. Granted, sound burst doesnt have the narrow focus of "evil" or "undead", but given what most parties fight it is a silly restriction and just makes your spell more powerful (both allow for a save to be stunned).
Further, the only spells powered by good usually do extra damage to undead by using a higher die type. You specifically mention channeling positive energy, which reminds me of a "Cure" Spell.
I think your spell should lose the stun but gain a capacity as a healing spell (albeit weaker, but at range). Dont step on sound burst's feet as a stunning 2nd level spell, make your own style.
Holy Bolt
Conjuration (Healing)
Level: Clr 2, Good 2, Mys 1
Components: V, S, DF
Casting Time: 1 action
Range: Close (25 + 5ft/2levels)
Target: 1 or more creatures, no two of which can be more than 15 ft apart
Duration: Instantaneous
Saving Throw: Will Half (harmless) (see text)
Spell Resistance: Yes (harmless)
You channel positive energy into bolts which strike their targets unerringly. The bolt strikes unerringly, even if the target is in melee or has anything less than total cover or concealment. Specific parts of a creature cannot be singled out. Inanimate objects (locks, etc) cannot be damaged by the spell.
These bolts cure 1d4 points of damage and for every two levels of experience past 1st, you gain an additional bolt. You have two at 3rd level, three at 5th level, four at 7th level, and the maximum of 5 bolts at 9th level or higher. If you shoot multiple bolts, you can have them strike a single creature or several creatures. A single bolt can strike only one creature. You must designate targets before you for SR or roll damage.
Since undead are powered by negative energy, this spell deals damage to them instead of curing their wounds and roll d6 instead of d4. An undead creature can attempt a Will save to take half damage.
Comparison:
Cure Moderate Wounds (10th level caster): 2d8+10 = 12-28 pts
Holy Bolt (10th level caster): 5d4 = 5-20 pts, but can be cast at range.
Technik