Many issues with the uninstaller were fixed in Gamma 4 and 5, like it leaving behind data that would make re-install impossible. So you would need the gamma 5 version of the uninstall file at least in place, in order to uninstall VaultWiki 4 fully.
I'm not sure what your particular reasons for uninstalling at this point are (the last I heard was about 3 months ago when a bug you had deleting comments was confirmed resolved by you), but it is unfortunate that you have not kept up with the new releases. There have been many fixes and improvements since Gamma 2:
Code:
4.0.0 Gamma 5
=============
- New Feature: Installer adds 1 public area to help get started
- New Feature: Most Wiki Contributions tab for XenForo Members list
- New Feature: Enable/Disable Reporting for Wiki content
- New Feature: Enable/Disable Wiki Subscriptions
- New Feature: Enable/Disable RSS Feeds
- New Feature: Setting for Maximum Contributors Displayed
- Changed: installer adds 1 system area for pre-sets
- Changed: minimum packet requirement based on expected query size
- Fixed Bug: Serious - can't delete subscriptions
- Fixed Bug: missing descriptions of protect options
- Fixed Bug: collaboration prevention blocks wiki moderators
- Fixed Bug: fatal error with reputation enabled in vB
- Fixed Bug: wiki items break "Activity Stream" forum block in vB
- Fixed Bug: phrases missing for wiki block config in vB
- Fixed Bug: fatal error removing book chapters
- Fixed Bug: read more link points to forum home
- Fixed Bug: wiki pages not showing in Activity Stream in vB
- Fixed Bug: Create tab uses options from first area only
- Fixed Bug: Create tab circumvents area's allowed prefixes
- Fixed Bug: Preview button only works once in vB < 4.1.4
- Fixed Bug: URL conflicts between attachments may appear ambiguous
- Fixed Bug: formatting issues on Special:ImageList
- Fixed Bug: message too long error in WYSIWYG mode in XF
- Fixed Bug: moderator auth not showing in vB4
- Fixed Bug: imported attachments from vB3 are empty
- Fixed Bug: pagenav wraps to new line in XF
- Fixed Bug: Settings > Notifications don't do anything
- Fixed Bug: wiki integration shows anyway on some error pages
- Fixed Bug: URLs with ASCII-range special characters are double-encoded
- Fixed Bug: possible editor button conflicts in XF
- Fixed Bug: file browser won't open after canceled upload
- Fixed Bug: AJAX prefix delete doesn't update the list
- Fixed Bug: IMG tags don't work in wiki pages in XF
- Fixed Bug: BB-Codes not translated in pages during VW3 import
- Fixed Bug: VaultWiki TABLE BB-Code overwrites vB4 TABLE on install
- Fixed Bug: text with ASCII-range special characters is double-encoded in XF
- Fixed Bug: subscriptions only use default notification type
- Fixed Bug: changes on Subscribe tab don't save
- Fixed Bug: invalid user ID on Special:Contributions
- Fixed Bug: AJAX prefix edit form breaks after first dialog
- Fixed Bug: database error entering BB-Code tag for prefix
- Fixed Bug: no permission to tag wiki pages in vB4
- Fixed Bug: reverting permissions redirects to non-existent page
- Fixed Bug: file browser won't open in some browsers
- Fixed Bug: area's content-related options don't save
- Fixed Bug: user subscription preferences don't change default view
- Fixed Bug: improper new line rendering for wiki index
- Fixed Bug: after AJAX area edit, area doesn't reappear in the list
- Fixed Bug: phrase missing for wiki disabled state
- Fixed Bug: temporary tables not removed by uninstall
- Fixed Bug: database error reverting CSS in vB4
- Fixed Bug: invalid argument for pre-Gamma-4 wiki activity block if never edited
4.0.0 Gamma 4
=============
- New Feature: Lite Mode
- New Feature: Add First Post when Starting Discussion
- New Feature: Use Wiki Sidebar Blocks as Forum Widgets
- New Feature: Synonyms for Page Sections
- New Feature: Check page existence with [VAR]id|Search for Title[/VAR]
- New Feature: Language Icons Automatically Select
- New Feature: File Health Check / Suspect File Versions
- Changed: compatibility with [bd] Widget Framework
- Changed: compatibility with dbSEO
- Changed: reduced up to 3 queries in vB
- Fixed Bug: can only choose Special for new pages
- Fixed Bug: empty subscription mails in XF
- Fixed Bug: subscription mails don't use user language
- Fixed Bug: database error hard-deleting soft-deleted comments
- Fixed Bug: page can be too long for editor switch in XF
- Fixed Bug: bb-code options cache doesn't update in XF
- Fixed Bug: cache doesn't rebuild if not currently loaded
- Fixed Bug: extra line breaks in plainChildren blocks in XF
- Fixed Bug: subscription mark is too large in XF
- Fixed Bug: can't update text via URL Conflicts admin page
- Fixed Bug: regression - wiki link previews don't work
- Fixed Bug: list preview can be longer than list
- Fixed Bug: 1 extra query due to common specials not cached
- Fixed Bug: some caches never load from datastore
- Fixed Bug: PLAIN doesn't work in wiki pages in XF
- Fixed Bug: missing link to RSS feeds
- Fixed Bug: CSS changes never apply in vB3
- Fixed Bug: forum RSS feeds broken in XF
- Fixed Bug: regression - all section edits are mismatches
- Fixed Bug: empty sub-forum lists on forum list in XF
4.0.0 Gamma 3
=============
- New Feature: Setting to Turn Wiki Sidebar On/Off
- New Feature: Disable Individual Wiki Content-Types
- New Feature: Headline Links
- Changed: updated to YUI 3.15.0
- Changed: moderation controls use standards (XF)
- Changed: animated section jumps
- Fixed Bug: XSS vulnerability (vB)
- Fixed Bug: island pages inaccessible if pretty URLs on (vB)
- Fixed Bug: collapse doesn't work for table of contents (vB)
- Fixed Bug: uncached templates (vB)
- Fixed Bug: top control doesn't jump to top
- Fixed Bug: special page headlines don't use icons
- Fixed Bug: editor double-encodes UTF-8 chars (XF)
- Fixed Bug: Legacy code not parsed (XF)
- Fixed Bug: search results not styled (vB4)
- Fixed Bug: bb_attach.gif is missing
- Fixed Bug: comments not imported from VW3
- Fixed Bug: video & image buttons missing from editor (vB)
- Fixed Bug: imported areas have comments disabled
- Fixed Bug: island URLs break after upgrade from VW3
- Fixed Bug: no permission to add attachments to comments (vB4)
- Fixed Bug: page list eats up memory
- Fixed Bug: autolink discovery slow for long page lists
- Fixed Bug: database error viewing Special:MostContributions
- Fixed Bug: install hangs on attach storage error
- Fixed Bug: changing area root corrupts childlist cache
- Fixed Bug: some integration types missing (vB)
- Fixed Bug: vw_path needs index for path
- Fixed Bug: template meta tags not working correctly (vB)
More importantly, the Gamma 2 release was found to be insecure several months ago, and all VW4+vB users were advised to move to at least Gamma 3. The attack vector was very easy to exploit according to the announcement. So if you are not removing this completely, or are re-installing after getting your database clean, you really need to do so against the new version.
Should you want to remove version 3.0.20, rather than just roll back to it, you need the patch from this blog entry:
https://www.vaultwiki.org/blogs/56/#Over-Time
If you have tried to remove version 3 without using this patch, a remaining VaultWiki 4 installation may become unusable. At this point in time version 3.0.20 has already reached its end of life. It is no longer receiving bug fixes or security updates, it is not compatible with vBulletin 4.2.1 or higher, or PHP 5.4 or higher.