Actually, adding attack modifiers to grapple checks only contradicts part of the self-contradictory FAQ.
Main 3.5e FAQ, page 20, "Vow of Poverty" entry
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The touch attack made to start a grapple is an attack roll (so the bonus would apply to this roll), but a grapple check is not an attack roll, and thus the bonus wouldn’t apply to the grapple check.
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Main 3.5e FAQ, page 29, "Grappling while prone" entry
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Bob has to win an opposed grapple check against Grog (still at –4 for being prone) to stand up.
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So in one entry, written by the new sage, Andy Collins, attack modifiers (like the Exalted bonus from VoP) do not apply to grapple checks. In an older entry, written by the previous sage, Skip Williams, attack modifiers (like that -4 while prone) do apply to grapple checks.
The PH says a grapple check is like a melee attack roll, then it shows the difference (a grapple check has a different size modifier than normal attack rolls). It does not list any other differences.
It's interesting to contrast the old 3e FAQ entries about grappling, which include auto-fail on a natural 1, auto-success on a natural 20, with Skip Williams' recent Rules of the Game articles. Skip has been wildly inconsistent on this, and Andy Collins only adds to the confusion.
I agree with Legildur that you should ignore the FAQ on this topic.
Just read the PH rules and treat a grapple check like a melee attack roll with a different size modifier. All the usual things that apply to melee attacks should also apply to grapple checks, including bonuses, penalties, double damage on Spirited Charge, Power Attack (as unarmed strike), True Strike, Prayer, Bless, auto-fail on a natural 1, auto-success on a natural 20, and critical threat on a natural 20.
But I'll respect differing opinions, especially since the so-called experts can't agree.