When you install these air filters what do you do with the oil over flow hose that goes into the stock air box?

First of all cbass78 itis great to see onother member from Louisiana here. If you put yourself on the member map it would make it easier for others from Louisiana to find you. Also I would be honored if you would join the "Louisiana Social Group". Go to community then click on social groups.
Now to your questio:
When you install these air filters what do you do with the oil over flow hose that goes into the stock air box?
You install a breather in its place.
http://www.denniskirk.com/jsp/product_catalog/Product.jsp?skuId=&store=Main&catId=414&productId=p301756&leafCatId=&mmyId=

Do you have to re-jet if you do a pod or k&n?

Yes a rjet is reccomended as the increased airflow makes the mixture leaner.

http://www.ninjette.org/forums/showthread.php?t=11899

Will that filter work with the pregen bikes as well?

sorry, I don't know the answer to that if you're talking about the DIY I linked.