I replaced my 1997 toyota 4runner factory door speakers over the weekend with polk audio 6.5(front) 5.25(rear)?

Its nothing you did wrong. The speakers from 14yrs ago, they are made from different materials than what the ones we use, are these days. So there will be a sound difference and less bass coming out. So you might have to add a sub..but did you get the 2-way or 3-way speakers? Those will produce different bass levels and overall sound quality too. Something to look at.