is PDF::Manipulate (rather, PDF::Manipulate::X) an OK name? (Contra: Verb as 2nd term? Too long? Negative connotations?)
"Manipulate" seems OK to me. If you think it is overly long then "Manip" is also fine (See Date::Manip, Bit::Manip, et al).
I considered "Parser", or "Wielder", or "ReadWrite", but like them even less.
Simply, "Edit"?
Honestly, it's the ::X and ::X2 which are slightly more confusing anyway. I would probably be more inclined to go with PDF::Foo::Compat for the drop-in replacement one and just PDF::Foo for the forward-looking one (where Foo is one of Manipulate/Manip/Edit/...). How does that sound?