You appear to be running some rather old versions of some SARE (and other) rule sets. It also looks like you have incomplete SARE rulesets, probably something like having a -1 file without the corresponding (and required) -0 file.
All of those warnings were fixed in the SARE rules that are valid for 3.0. They still exist (deliberately) in a file are two that are NOT supposed to be used with 3.0. I would start by cleaning up your local rules. Look at the descriptions on the SARE rules page and see which rule sets you should and shouldn't have, and get the latest versions. Make sure that you check the descriptions for dependencies too. Also consider redownloading some of the other rule sets. Looks like you have bogus-virus-warnings there; I think it has been updated to fix many if not all of the warnings. Another thing to check. If you dodn't blow away your 2.63 install before ding the 3.0 install, 3.0 might be picking up your old rules from 2.63. It seems that the installs for different platforms (and different releases of the same platform) tend to move around on where the rules are supposed to be. SA can sometimes end up seeing both old and new rules, which is a bad thing. Now, I don't see anything in those lint warnings that should be keeping things from working, but if you have the wrong rules running you probably won't get very good results. Loren