Are you new to the forums? PLEASE introduce yourself in the member area so we can welcome you properly, thank you.
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You should install SMF 1.1.8 as it addressed alot of security issues. From seeing what you encountered, you can export the members table via phpMyAdmin, and install the new forum and import the members table into the new forum.Also in the future, if you have mods installed, be sure to uninstall the mod first before deleting its files, especially Flash Chat, since it has db information that goes with it.
If you keep the Attachments folder and the two Settings.php files and wipe everything else out and re-upload all the files again from the install zip (Excluding the Settings.php and the Attachments folder) you should have all clean files and still the same database with all your attachments. If you have mods installed you might get errors on them because they would not be installed anymore but the info for them will be in the database.
Well, seeing that you two have been infected, I suggest you read this topic first.http://www.simplemachines.org/community/index.php?topic=309717.0