Just installed my long tube headers on my 04, lost a lot of bottom end, no leaks or clearance issues, haven't got my tune yet, but will this clear up with a tune?

 

A tune will help it a but, but no not really. Long tubes are good for a good amount of horsepower at the top end but at the cost of losing some bottom end torque.

A lot of people don't research them before they buy, and aren't visiting the top end a lot, the stories end up a lot like yours.