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I am not entirely sure if this is a transmission problem or not, but i will leave that to you all to decide  

After my last oil change I felt a jerk while driving.  My RPM's dropped suddenly and then when back to normal.  This doesn't happen too often, but enough for me to worry about it.  Yesterday instead of dropping it spiked and while I was warming my car yesterday morning the enging cut off all together.  
 At each drop I hear a clicking sound under the center of the dashboard.  I also thought this could be the alternator.

What are your thoughts?  Thanks for any and all help, I really appreciate it.  

it sounds like you may be having an ignition power loss. possibly a relay or a bad connection. there are small businesses that offer a free initial diagnostic.  
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