Depending on your application, you can get a front or a rear sump oil pan and pump pickup tube. It may help to reverse the sump end. I had to do this on a spotter truck I put a 5. 9 in for a customer. The 3. 9s are the same way.
The bellhousings and flywheels will interchange between the 3. 9 and 5. 9s. The accessories bolt on the same way also. I plan a 3. 9 in a Wrangler someday, using a 4500 or 5600 trans and transfer case out of a Dodge/Cummins.