Hello Mranderson,
Welcome to the Vista Forums.
As for the flash player: In x64 you will have 2 versions of IE. One is 64bit and one is 32 bit. Flash will only install in the 32 bit version. Adobe has said they're working on a 64 bit version, but trees move faster than they seem to. But I digress. Make sure you are using the 32 bit version. The shortcut for x64 should say so. You can also check by clicking on the arrow next to the question mark and selecting about. If the 64 bit part is missing, your in 32 bit.
Don't know anything about messenger, sorry. Someone here ought to be able to help you though.
First thing I do for the links is to go to Control Panel/Default Programs/Set Your Default Programs and set IE as default (or whatever browser you are using). See if that works.
Hope this helps.
Gary