I am putting some BUB jug huggers on my 03' softail standard. Do I need to upgrade my stock air cleaner for better air flow?

 

For improved air flow? Yes. You didn't mention if your bike is EFI or carbed. If carbed, rejet. If EFI and Stage I is as far as you intend to go, you should look in to the available "electronic jet kit" fuel management systems like Dobeck, Dynatek, Cobra. Dobeck manufactures units for private labels like Wiseco, Two Brothers, Arlen Ness, etc. A Stage I upgrade will lean out the A/F and you will need a system like one of the above to restore the A/F to a proper ratio. No need to spend more money on more sophisticated systems that require dyno tuning for a Stage I upgrade. JMHO.