Adam,
Ok, you have the air purge button on the control panel. That gives you an easy way to purge the air after you change the fuel filters. I agree that your pre-filter/strainer look very good and should not need to be replaced or cleaned. If the primary filter only has 5,000 miles it should be OK. That primary filter is a little strange now that I can see it in this latest picture. BTW, my mistake on the P/N for the pre-filter, it is a 300200 and they can be purchased but hard to find.
As Gerald pointed out, the original OEM Racor filter was replaced with a separate bowl w/water purge and sensor wire for detecting the water in the bottom of the bowl. That replacement filter can be purchased under Wix P/N 33621 or Donaldson P558800, but you will need the bowl conversion that Gerald referenced in his earlier post. Also, as Gerald noted the Baldwin BF1252 can be used without the separate bowl, but does not have the water purge connection. It does have a manual value for draining water.
I would consider just replacing the current filter with the Baldwin just because it will save you the cost of the bowl conversion. Changing the filter is just like an oil filter in the car. Do not prefill with diesel and be sure and lubricate the "O" ring before installation. Do not overtighen per the instructions on the outside of the filter housing. After you have completed the installation, hit the purge button and start your engine.
My big concern is if that your Primary Racor fuel filter could be very old (they have not been made for 10 years or more)... Could that be possible?