This is right on, except when redoing your cooling system - i would drop in the bigger 6 cylinder radiator. To keep your engine cool, down around 180 degrees - you will need the big radiator.
I dropped an all aluminum single row one I found online for about $200 shipped and put a Ford Taurus Fan that I bought for $28 from the junkyard, and I have NEVER had any issues with cooling; well, that is not true; one time I did overheat, when I forgot to reconnect the fan after changing the alternator, but it was not because of the fan or the radiator!
In any case, I agree with both posters; flush the cooling system, change the thermostat (mine was done when i bought the Jeep and would not close at all). I used a Robert Shaw 190* thermostat in mine and have not had any issues (and this is living in Miami, where the weather is hot year round).
If everything checks out $4000 is a fair price. Check gas tank skid plate for rust holes. If possible check fuel pressure. I just had to replace fuel pump module on my 97' (burnt wires in module).
I also had issues with the fuel pump in my YJ when I got it 2 years ago... So if you can check the fuel pressure (which is really easy to do), I recommend you do it.
Felipe