Apologies for the confusion! To answer in order:
- Each attribute adds (or subtracts) GOO-P, and it's all totaled up along with the modifier for species.
- Skill Base and Skill Gain aren't dealt with until Step #7 (pg. 54); which is why Step #3 (pg. 12) directs one to only worry about the attribute's value and GOO-P modifier for that step. The others are addressed later.
- The cost of each evolution step is listed both on the relevant pages (pgs. 38-40) and is cumulative (pg. 38); each is generally 2-5 GOO-P. If a step is n/a that means that though some species start with that trait, there's normally no evolution route to it. With the example, a limbless character (i.e. a snake or worm, generally) who wants two humanoid legs has to go along the evolution route to purchase forelimbs (5-GOO-P), quadrupedal (5 GOO-P), semi-bipedal (5 GOO-P), and bipedal (5 GOO-P), which adds up to a total of 20 GOO-P. But a character who wants the Cloaked trait has to pick up Inhuman (2 GOO-P), then Kemonomimi (3 GOO-P), and finally Cloaked (3 GOO-P), for a total of 8 GOO-P.