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Transmission is shifting a little high, and downshifting a little rough after headgasket job...

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Well I just finished a head gasket job on my 1998 Subaru Legacy Outback wagon...

 

I noticed that it is shifting a little high and rough and down shifting a little rough...

 

I am thinking that this has something to do with the second cable on the throttle body...  maybe it's not adjusted correctly?

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The 2nd cable is for the cruise control.  When you pulled the engine did the torque converter come with it a little and leak some fluid?  Maybe you just need a little more fluid to top it off?

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