Help: I think i deleted some imp files

1) i deleted a lot of applications that i do not use to make more space. I followed steps online to deleted application support data etc. What has happened now is that i see a ? on my doc. I can remove the ? but when i reboot the mac they appear again. What should i do?
2) I am also having issue saving my mail client preferences. It is also not allowing me to delete my current gmail account. It does allow me to delete but if quit and re open the mail client it the gmail account is back again
3) I unable to sign out of itunes store or mac app store.

Sig,
if you must know the whole story-
I got a new mac and I am selling this one off ( this is 2009 MBP running 10.7.1). I had installed Logic pro and supporting jam pack, apple loops etc. with 50 GB data; ivory ( and other software instruments) with about 77 GB of data . I deleted that and couple of other smaller apps which i know my friend wont use. To delete logic and all its support files i had to follow some steps suggested by some one online.
After that I ended up with the issues above.
I checked to see if i have a com.apple.doc.plist - I do not have that file. some have said to delete that file to fix it but i did not see that file
Instead i had a com.apple.docfixup.plist. i removed that file but it did not help either.

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Help: I think i deleted some imp files

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