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There will be differences with the input shaft, and possibly bell housing, it depends on the transmission model and engine you are trying to match up, not every 1990 had the same engine or transmission.
Good news is that no matter what you decide you want there is a conversion kit available, just check out the mustang mod sites.
What else can I help you with?
What transmission is in a Mustang?
The Mustang GT (2011 model) has a 6-speed manual transmission standard and a 6-speed automatic transmission optional. The 2010 Mustang GT had a 5-speed manual transmission standard and a 5-speed automatic transmission optional.
What is the transmission on a 1987 Mustang?
The 1987 Ford Mustang came with a T-5 five-speed manual or optional automatic transmission.
What kind of transmission does the 2007 Ford Mustang have?
The 2007 Ford Mustang has a 5-speed manual.
What kind of transmission does the 2003 Ford Mustang have?
The 2003 Ford Mustang has a 5-speed manual.
What kind of transmission does the 2009 Ford Mustang have?
The 2009 Ford Mustang has a 5-speed manual.
What kind of transmission does the 2014 Ford Mustang have?
The 2014 Ford Mustang has a 6-speed manual.
What kind of transmission does the 2006 Ford Mustang have?
The 2006 Ford Mustang has a 5-speed manual.
What kind of transmission does the 2010 Ford Mustang have?
The 2010 Ford Mustang has a 5-speed manual.
What kind of transmission does the 2005 Ford Mustang have?
The 2005 Ford Mustang has a 5-speed manual.
What kind of transmission does the 2004 Ford Mustang have?
The 2004 Ford Mustang has a 5-speed manual.
What kind of transmission does the 2002 Ford Mustang have?
The 2002 Ford Mustang has a 5-speed manual.
What kind of transmission does the 2013 Ford Mustang have?
The 2013 Ford Mustang has a 6-speed manual.
