The Jeep could have been through deep water that was over the transmission height without the breather lines extended.
To edit original question....Jeep Wrangler 2005 manual transmission
The 2009 Jeep Wrangler has a 6-speed manual.
The 2012 Jeep Wrangler has a 6-speed manual.
The 2011 Jeep Wrangler has a 6-speed manual.
The 2005 Jeep Wrangler has a 6-speed manual.
The 2008 Jeep Wrangler has a 6-speed manual.
The 2010 Jeep Wrangler has a 6-speed manual.
The 2001 Jeep Wrangler has a 5-speed manual.
The 2003 Jeep Wrangler has a 5-speed manual.
The 2007 Jeep Wrangler has a 6-speed manual.
The 2014 Jeep Wrangler has a 6-speed manual.
The 2013 Jeep Wrangler has a 6-speed manual.