The fuel filter is located in the fuel tank with the pump. It's not really designed to be replaced but it certainly can be if needed. The tank just has to be dropped. Why are they wanting to replace it anyway?? Are you having some sort of issue with your truck that makes them think it needs replacing? If not, it doesn't need replacing and even if you are I would look elsewhere before I messed with the in-tank filter. Like starting with a thorough throttle body clean, running some Sea Foam, and a plug change if it's time for one. All things you can do yourself.
My understanding about the O2 sensor is that it's pretty simple. Unplug, unscrew, repeat in reverse and done. The only kink is that it might be a little hard to break loose. Might even need a little heat thrown to it but that's something an independent shop could fairly cheaply do if you can't. The sensors do vary in price a little depending whether it's an upstream or downstream sensor.
I would see what they have to say about the rear seal. Are you talking about the rear diff? That work can get a little expensive, depending on the problem. But it doesn't necessarily have to be. I just had my mechanic fix a leaking rear pinion seal and it cost me $75. Of course, that's best case scenario.
So what else are they trying to do that adds up to $4,000??
Grrrr....my bad. I just realized you are rocking a Cummins so my response is not very helpful, lol. I'm clueless when it comes to diesels but this looks like a good how-to on the fuel pump. It says 15 minutes!
I don't know but I couldn't imagine the O2 sensor swap being all that different unless it is just extremely hard to get to for some reason.
Maybe that's a little help. Not as much help as I originally intended, lol.