Intrusion Suspected, Advice Sought

[JohnG]

I run OS X 10.3.7 on a PowerMac MDD G4 on a cable broadband connection. 
I have reason to think my system has been tampered with. Security 
features in Mac OS X have been left unlocked (Preference Pane - Users) 
even though a master lock has always been set in the Security 
Preference Pane. This locks all other important preference panes which 
could be tampered with. Also permissions have been reset at every boot 
in my working directory. I've worked on this machine for about 17 
months, and I know its rhythms and what should be what. The permissions 
problem is persistent and new. I do not think I am being paranoid or 
alarmist. I have always had a NAT router, commercial firewall, and 
virus protection.

The only thing I can think of is a hidden *nix program from a 
downloaded program (shareware/freeware) (I have scanned all packages 
for viruses). I am almost positive it did not come via e-mail. I say 
almost because I have been receiving odd e-mails that are totally blank 
and have no information I can find. Conceivably, it could have been a 
hacker. If so, that person was very skillful in getting in and only 
left small traces of poking around.

I assume your advice will be to do a clean re-install of both system 
and programs. My question is how do I re-import the data from full 
backup (probably also containing whatever it is) without further 
jeopardizing my system? Any other advice, tips, or pointers to FreeBSD 
programs I could run on Mac would be greatly appreciated.

John Scherb