I finally installed my new deck and got all the bugs fixed but my lower frequencies on my sub aren't as good as when I had a lc8 and my oem stereo.

This version of pioneer stereos don't have a loudness feature and I have the crossover for my sub off. On my amp they are at 25hz and 100hz. I have a noise filter for the engine noise my sub had but it sounded the same without the filter.

Same settings on the amp as when I had my oem stereo.

Do you guys have any suggestions?

Do you have the sub enabled (turned on) on the unit?

Yes

turn off the xover from your amp and use the head unit xover, low pass at 80hz try 12~18dB slope.  make sure the speaker level for the sub is set to desirable level.  You can also bump up 50~80hz via the EQ (ensure you have HPF set for your mid).