So a clocksmith wizard get a clockwork familiar via clockwork bond:
A clocksmith forms a bond with one of his clockwork creations and begins play with a constructed familiar. He must select this familiar as his arcane bond. The constructed familiar functions as a typical familiar of its type except as noted here.
The construct familiar is always a construct with the clockwork subtype. A construct familiar grants only half of its typical bonus (minimum +1 bonus) from its special familiar ability to its master.
This alters arcane bond.
The subtype lists:
Clockworks are constructs created through a fusion of magic and technology. They have the following traits unless otherwise noted.
Winding (Ex) Clockwork constructs must be wound with special keys in order to function. As a general rule, a fully wound clockwork can remain active for 1 day per Hit Die, but shorter or longer durations are possible.
Vulnerable to Electricity: Clockwork constructs take 150% as much damage as normal from electricity attacks.
Swift Reactions (Ex) Clockwork constructs generally react much more swiftly than other constructs. They gain Improved Initiative and Lightning Reflexes as bonus feats, and gain a +2 dodge bonus to AC.
Difficult to Create (Ex) The time and gp cost required to create a clockwork is 150% of normal. Construction requirements in individual clockwork monster entries are already increased.
Clockwork Augmentations
In addition to the standard special abilities and qualities granted by the clockwork subtype, many clockwork designs incorporate more abilities designed by their engineers. The following examples are intended to help GMs build new clockworks or modify existing ones.
Some of the most common clockwork special abilities have been gathered in this section along with a number of new ones.
Charged (Ex): Equipped with a static generator, a clockwork with this special ability deals an additional 1d6 points of electricity damage with all natural attacks and melee weapons it has. Source PAP123
Efficient Winding (Ex): Built for long missions, a clockwork with this special ability can function for 2 days per Hit Die each time it’s wound. If the creature’s CR is 11 or higher, it can function for 3 days per Hit Die each time it is wound. Source PAP123
Embedded Ioun Stone (Ex): As a full-round action, an ioun stone can be embedded in (or removed from) a slot in the clockwork creature (usually on its forehead). It is possible to embed or remove an ioun stone only if the clockwork is helpless, pinned, or willing. The clockwork gains the benefit of the ioun stone, including its resonant power. Source PAP123
Grind (Ex): A clockwork with this special attack deals additional slashing damage when it makes a successful grapple combat maneuver check because of many twisting gears and churning pistons in its body. This additional damage is equal to 1d4 points (1d6 if Large, 1d8 if Huge, 2d6 if Gargantuan, or 3d6 if Colossal) plus 1-1/2 the creature’s Strength bonus. Source PAP123
Integrated Firearm (Ex): One of the clockwork’s arms ends in a firearm. The firearm generally functions as a pistol or musket intended for a creature of the clockwork’s size, but nearly any firearm of suitable size is possible. The clockwork is considered proficient with the weapon. The clockwork can reload an integrated one-handed firearm as a swift action and an integrated two-handed firearm as a move action. As a standard action, the clockwork can remove the broken condition from an integrated firearm, provided that the condition resulted from a misfire. A clockwork usually has 10 rounds of ammunition and gunpowder stored within a reloading mechanism. Source PAP123
Proficient (Ex): A clockwork with this special ability is proficient with all simple and martial weapons. The clockwork must have humanlike hands in order to gain this ability. Source PAP123
Repair Clockwork (Ex): Clockworks with this special ability are adept at repairing other clockwork constructs. As a standard action that does not provoke an attack of opportunity, the clockwork can repair damage done to either itself or an adjacent clockwork creature, restoring 1d10 hit points to the target. If the repairing creature’s CR is 11 or higher, the amount of hit points restored increases to 2d10. Source PAP123
Self-Destruction (Ex): When the hit points of a creature with this special ability are reduced to 10% of its total or less but are still above 0, the creature self-destructs on its next turn, bursting in an explosion of metal scraps and steam in a 20-foot-radius burst. The damage dealt is equal to 1d6 points for each Hit Die above 5 the construct has (clockworks with 5 or fewer Hit Dice cannot gain this ability). Half of this damage is fire damage and half is slashing damage. A target that succeeds at a Reflex save (DC = 10 + half the clockwork’s Hit Dice + the creature’s Constitution modifier [usually 0]) takes half damage. Source PAP123
Standby (Ex): A clockwork creature with this special ability can place itself on standby as a standard action. While on standby, the clockwork creature cannot move or take any actions. It remains aware of its surroundings but takes a –4 penalty on Perception checks. Time spent on standby does not count against the clockwork’s wind-down duration. The clockwork can exit standby as a swift action. If it does so to initiate combat, it gains a +4 racial bonus on its Initiative check. Source PAP123
Tough Alloys (Ex): The clockwork gains Toughness as a bonus feat.
If the wizard wanted to upgrade his familiar with some of these options; what should the cost be?
these options are not for players to begin with, which is why they don't have a cost the same as you won't see a cost to gaining a template. it's a way for the GM to alter his encounters:
(from your own quote)
"In addition to the standard special abilities and qualities granted by the clockwork subtype, many clockwork designs incorporate more abilities designed by their engineers. The following examples are intended to help GMs build new clockworks or modify existing ones."
if the gm want to let you make one of these adjustments he need to figure out how much he would price it.
(as for me, i would price it with an appropriate quest or side hook, it's much more rewarding having your familiar shoot the musket leg you got him by defeating 'Pierre the pirate parrot' then just paying X,000 gp and spending a day or two to craft)
Id absolutely do quests to unlock schematics. Much more rewarding