The 99's had two different fuel pumps. A returnless and a return style. Later 99's had the returnless, but I can't tell you from what date that occured. Yes you can look on the door jam for the production date.
As far as how long it takes. It took me about 3 hrs the first time including a trip to the store for some tin snips. I also fought with figuring out how to get the rear seat cushion out and how to undo the center sholder belt. After that it was pretty easy. I can now do it in under 1 hour, start to finish. The how-to is pretty good, though I'd change a part or two in it slightly.
I don't think there is anything you can do about the fuel pump life. My recommendation is to keep the tank about 1/4 all the time, this should extend the life (I don't follow this rule due to racing though). I'd recommend just buying the pump itself from
BAT. They sell it for 75 or something like that. Ford only sales the sending unit (sump), and the pump for $225 or something like that. Basically all you have to do to save yourself some money is take out a few more hex screws and pry some plastic clips apart and insert the new pump. Saves you about $100!