@Paladox pointed out that the web-based upgrader is failing for the HitCounters extension. While the upgrade appears to progress normally, the schema updates for HitCounters aren't made.
Also of note, I had to disable SemanticForms to even get this far since on the mw-config/?page=ExistingWiki page I ran into the following error:
[2130fe41] /w/mw-config/?page=ExistingWiki MWException from line 185 of /var/www/w/includes/Hooks.php: Invalid callback SFParserFunctions::registerFunctions in hooks for ParserFirstCallInit
Backtrace:
#0 /var/www/w/includes/parser/Parser.php(310): Hooks::run(string, array)
#1 /var/www/w/includes/parser/Parser.php(320): Parser->firstCallInit()
#2 /var/www/w/includes/parser/Parser.php(5025): Parser->clearState()
#3 /var/www/w/includes/parser/Parser.php(405): Parser->startParse(Title, ParserOptions, integer, boolean)
#4 /var/www/w/includes/installer/Installer.php(630): Parser->parse(string, Title, ParserOptions, boolean)
#5 /var/www/w/includes/installer/WebInstaller.php(676): Installer->parse(string, boolean)
#6 /var/www/w/includes/installer/WebInstallerPage.php(392): WebInstaller->getInfoBox(string)
#7 /var/www/w/includes/installer/WebInstallerPage.php(380): WebInstallerExistingWiki->showKeyForm()
#8 /var/www/w/includes/installer/WebInstaller.php(280): WebInstallerExistingWiki->execute()
#9 /var/www/w/mw-config/index.php(77): WebInstaller->execute(array)
#10 /var/www/w/mw-config/index.php(36): wfInstallerMain()
#11 {main}