The clay golem body costs 1,500 gp. The total construction cost of a clay golem (including body cost) is 21,500. Were one to purchase a clay golem from the local clay golem vendor ("Step right up! Getchyer berserking buddies here! Guaranteed to betray you when you need 'em most!"), his price would be 41,500 gp. None of these values change if a golem manual is used because
The golem manual mitigates only some of the hardships of golem creation
With or without a manual, the golem's creator still pays for the golem body. In addition to granting a a +5 competence bonus to the Craft skill check necessary to create the golem body, the manual, also functions as a spell trigger magic item capable of providing the spells necessary to create the golem but only to create that one golem. Even with a manual, the golem creator must either have these spells on his spell list or convince the DM that the Use Magic Device skill's activate a wand skill use is actually code for activate a spell trigger magic item then make Use Magic Device skill checks each day of golem creation for each spell.
What this really means is that the creator—who must still labor over the golem's creation for weeks or months—needn't prepare and expend the spells necessary for golem creation while working. The golem manual (iron), for example, makes it possible for a Wiz12 creator not to worry about where he's going to get 150 castings of polymorph any object.
The creator also doesn't need the feat Craft Construct when using the golem manual to create that one golem, which is useful, and using the golem manual means the creator can be a lower level than the golem's usual requirements mandate (i.e. minimum caster level 9 for a clay golem, 7 for a flesh, 12 for an iron, 11 for a stone). This is what makes the golem manual shine, allowing the creator a golem that may survive 1–4 levels alongside its master.
To summarize, a golem manual doesn't eliminate the golem's body cost, the golem's price, nor the time necessary to create the golem. It doesn't provide the spellcasting ability necessary to create the golem, yet it provides access to the necessary spells and reduces the caster level required to create the golem. It doesn't provide the feat Craft Construct except for the purposes of creating the lone golem the manual describes. "When the book's ashes are sprinkled upon the golem, it becomes fully animated," says the manual's description, but whether this eliminates the Spellcraft skill check necessary for the golem's creation is up to the GM.
While all this may seem to make a golem manual less than desirable, its ability to grant the user a minion with a Challenge Rating greater than the user's is sufficient to warrant them being, overall, pretty okay if the user also has the time and money necessary for constructing the minion in the first place. However, much of the utility of a golem manual disappears if the creator can succeed on a really high Craft skill check.1
1 "The [skill check] DC to create a magic item increases by 5 for each prerequisite the caster does not meet," it says here, so, for example, if a creature with the feat Craft Construct can succeed on a Craft skill check (DC 46) he can eliminate the clay golem's requirements of the spells animate objects, bless, commune, prayer, and resurrection, and maybe even the necessity of being caster level 11th (but ask the GM).