Replacing a claw attack with an unarmed strike
Sorry, but no. Unarmed strikes use a weird hybrid of the rules for manufactured and natural weapons, but for the purposes of full-attacks, they work like manufactured weapons. That is, you get iteratives with them, but if you can only combine them with natural weapons by making those natural weapons secondary (−5 attack penalty, only ½Str to damage).
The first rule that you quote is specifically about spells and effects. A full-attack is not either of those.
Claws and lack of offhand unarmed strikes
Feral Combat Training does mean that anything from the monk’s unarmed-strike-improving class features can apply to natural weapons, and that can include the bit about never being offhand.
However, claws and other natural weapons are never “offhand” to begin with. The term “offhand” only applies when using two-weapon fighting, and that combat option does not interact with natural weapons (aside from the attack penalty, which applies to all attacks). So the fact that the monk class feature, combined with Feral Combat Training, says that natural weapons are never offhand does not do anything because that was already true.
Instead of “main hand” and “offhand,” natural weapons are either “primary” or “secondary.” These are different. When combined with manufactured weapons (or unarmed strikes) in a given full-attack, all natural weapons are secondary: they receive the −5 penalty and get only ½Str to damage. Neither the monk class nor Feral Combat Training does anything about treating them as secondary or removing or reducing the penalties for being secondary.
So whether you have Feral Combat Training or not, your full-attack using unarmed strikes is:
Unarmed Strike, Claw (−5), Claw (−5), Claw (−5)
If you have Feral Combat Training, the claws do benefit from the improved base damage dice of unarmed strike, however, even if they’re still stuck with ½Str to damage.
Two-Weapon Fighting, Feral Combat Training
If you are actually using two-weapon fighting, the provision about monks never having offhand unarmed strikes meaningfully applies only to the unarmed strike. It “applies” to the claws, but does nothing for them.
So, for example, if your two weapons are a sai and an unarmed strike, and you have the Two-Weapon Fighting feat, your attack routine would be:
Sai (−2), unarmed strike (−2), claw (−5), claw (−5)
The unarmed strike would add your full Strength to its damage, however. Note that I assumed that the sai took up one of your claw-hands. I did not wish to get into the debate about whether one can use two unarmed strikes as part of two-weapon fighting.
You didn’t ask, but about Flurry of Blows
All of the statements above about full-attack apply equally well to flurry of blows, except that you need Feral Combat Training to use natural weapons in a flurry at all, and flurry of blows cannot be combined with two-weapon fighting because of Paizo nonsense.
For the record, monks, natural attacks, and how they combine, these are some of the worst things in Pathfinder. The rules are confusing, complicated, and the result works very poorly. I suggest you save yourself a headache and just... not.
All 3 games mandate making attacks from highest base attack bonus to lowest
Player's Handbook (2000) for Dungeons and Dragons, Third Edition on Full Attack says
If you get multiple attacks based on your base attack bonus, you must make the attacks in order from highest bonus to lowest. If you are using two weapons, you can strike with either weapon first. If you are using a double weapon, you can strike with either part of the weapon first. (124)
The Player's Handbook (2012) for Dungeons and Dragons 3.5 on Full Attack says
If you get multiple attacks because your base attack bonus is high enough, you must make the attacks in order from highest bonus to lowest. If you are using two weapons, you can strike with either weapon first. If you are using a double weapon, you can strike with either part of the weapon first. (143)
In the 4th printing of the Pathfinder Role-playing Game Core Rule Book (2010) the latter is repeated verbatim on Full Attack (187).
Thus, without further guidance, it seems reasonable that the player picks the order of his character's attacks if two or more attacks are tied for the same base attack bonus (such as when wielding two weapons). The player, however, can't pick the attacks that are made at less than the base attack bonus (e.g. the additional attack at +1 from a base attack bonus of +6) until after attacks have been made at the full base attack bonus.
The example D&D 3.5 character with a base attack bonus of +6, the feats Two-weapon Fighting and Improved Two-weapon Fighting, and affected by the spell haste taking the full attack action makes 1 attack with his primary weapon at his full base attack bonus, 1 attack with his off-hand weapon at his full base attack bonus, and 1 attack with either weapon at his full base attack bonus, and the character could make those attacks in any order. He then makes 1 attack with his primary weapon at his base attack bonus −5 and 1 attack with his off-hand weapon at his base attack bonus −5, and could make those attacks in any order.
The monk uses whichever he's using.
If the monk is both hasted and using Flurry of Blows, he adds an additional attack in his Flurry at the highest BAB in that Flurry. If, for some reason, he's not using Flurry of Blows (maybe he's using a non-monk weapon?), he adds an additional attack at the BAB in that full attack.