Just want to know if a factory sway bar will work with a nine inch.

Thats would depend on if your lower control arms are in the same location after the swap. If they are then probably it would work provided the bar clears the housing.

It was a pre fab rear and it bolted right in. I just dont know if the bar goes behind the rear or right under the center section.

As soon as I get the new bar I will fit it and post results. I dont think too many people run a nine inch but I will post anyway.

I use a hotchkis rear bar and it works fine with a Dana 60 (9.75" gear or somthin?).

It's been discussed before, mine wouldn't fit but others said theirs did.