Hi.  I have a 98 Legacy outback 2.5.  I just rebuilt the transmission on this car, so I know its not transmissions related.  I'm having trouble with a harsh 1-2 shift, and late upshifts after.  It doesn't do it all the time, but i have discovered its because of a voltage drop to the transmission that causes it. 
  
I have tried all the following:  New MAF, dropping resister, NEW TPS, used TCM and I have traced all the wires for HOURS, and see nothing grounded or cut. 
  
I have no idea what could be causing this.  Any ideas, no matter how crazy, are appreciated.