I think some of these questions come from a willful misinterpretation of the obvious spirit of the rules. As such I'm gonna get a bit snarky about it. Fair warning.
#1 - The Stacked Catch only applies if you already have another catch applying to your other Toughness powers. There are no other Toughness powers in #1, so the principle of biggest value catch applies, netting only a +5 value.
From a pure wording standpoint it says that you get a catch for "your toughness abilities" and PI is a toughness ability, therefore you should get a catch for the general group of abilities known as "toughness abilities", then you should get a stacked catch for PI, even though PI is the only ability you have. OBVIOUSLY this is not what is intended, but it is still a way in which it can be interpreted by someone trying exploit the system and should probably be clarified.
Another issue:
"Catches cannot reduce the cost of your Toughness powers below –1."
Because "Toughness" is the name of the sum of all powers in this heading it is not completely clear whether this applies to your toughness powers as a whole, or to each individually. Obviously you meant individually, but that is not clear from the text as written.
This also brings up another issue. By looking over how various creatures in OW are set up it is obvious that it doesn't matter how much the "The Catch" is "worth" if the only toughness power you have aside from PI is Inhuman Recovery then "The Catch" MUST be reduced to +1, and this applies before a Stacked Catch is applied. Similarly, if you have Inhuman Recovery and Inhuman Toughness then "The Catch" MUST be reduced to +2, no matter how much it is actually worth, all before a Stacked Catch is applied... Supernatural toughness and Inhuman Recovery and a Catch worth +5? Nope, must be reduced to +4.
HOWEVER, that is not what the text actually says. It merely says that Catches cannot reduce the cost of toughness powers below -1. It doesn't actually say that you can't have a catch worth more than the powers value.
I can forsee someone doing the following without realizing why it is wrong:
Inhuman Recovery -2
Inhuman Toughness -2
Physical Immunity -8
The Catch +5
The Catch (stacked) +5
Total: -3 (minimum -1 per power)
Should be:
Inhuman Recovery -2
Inhuman Toughness -2
Physical Immunity -8
The Catch +2
The Catch (stacked) +5
Total: -5