IPhone :: Restore Contacts And Apps Without ITunes

My iPhone was acting up so I backed it up and took it to the Apple Store. They promptly replaced it and told me not to restore it from the backup in iTunes. While I was certain I'd heard Apple/Mac's didn't get viruses, the Genius told me that whatever problem the iPhone had, may be embedded into the Contacts and restoring them may transfer the problem to my new phone. Sounds like a virus to me.

He said there's a way to retrieve the contacts from the PC without going through Itunes & if I do it this way, my virus program will filter out any "embedded problem." No, I did not backup my contacts to Outlook. I never needed them and just assumed they were being put there. HELP!! I no longer use a paper phone book--I had over 10 years of contacts in my iPhone and are somewhere on my PC. How can I get them on my new iPhone?

2nd question. How do I get all of my apps back, again, without restoring from prior backup? I tried to right click on my iPhone in iTunes and click restore purchases, but a funny thing happened...it transferred only one over??? I have at least 25 or 30.