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SBS 2003 reinstall

SBS 2003 crashed overnight: no system file...tried a number of things to recover, no luck. Hard drive OK, multiple windows file corruptions, so I tried running repair from CD1, no windows installations to found. Ran windows install and chose keep existing ntfs file system.  Windows came up but missing full to do list.  mmc won't run, missing snapins. Installation renamed existing sbs and sql server folders as old, created new user folders....
This is a small 7 user business w/ only one real role for server, run third party inventory mgmt software on top of sql server.  Original install had seperate drives and partitions for apps, data and logs.  Need to get sbs and sql server up asap and get third party app reinstalled and running. Help please.
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Yes, that's a possibility...what do you mean by "port over", can you be more specific, please?
By Port, I mean Copy. By definition though, copying is somewhat easy, Porting (as i call it) indicates probable anslysis you'll have to plough through due to likely  permissions issues on the new server since when you copy, the permissions and security settings are lost (of course).

Really, just a play on words. OK?    
OK ...I took your advice and installed sbs on a different a side note, i had already done this, but my plan was to 'port' over the files from the new drive to repair the original and that didn't work.  So I put that drive back in as primary and the old drive is still in the machine as the app partition is on is and is still viable.  Not much to 'port' other than AD (if possible) as all apps, data and logs were on seperate partiitions and drives.  Thanks
Oh yes, i forgot you had seperate drives and shares snd stuff. That was very handy!

All working now?
Yes, thanks...the server is up and running...a few AD issues to deal with.