Not exactly. Think about it for a second - the only way to really clean anything out of the tank is to completely remove it; if you don't, whatever's in there is just going to get trapped in the fuel filter.
Sea Foam can be used in fuel to help clean out the fuel system - everything forward of the filter up to the injectors. It's also good to use on the throttle body and intake to decarbonise them, the valves, and the combustion chambers. I actually ran some (finally found it locally!) through my XJ a couple of nights ago, and there's a very noticeable difference. It's much quieter now, a lack of urge at low revs is gone, and fuel economy seems slightly improved. I'll run some again (minus the fuel treatment) in a few weeks before I change the spark plugs.
Back to the issue at hand: the IAC is the Idle Air Controller. Looks kind of like a spark plug sticking up out of the intake manifold with a couple of wires coming off of it. You can pull it and try *gently* cleaning it out with some penetrating oil and/or PB Blaster; be sure not to tweak the little plunger (you'll see what I mean when you get it out) inside of it while doing this. Hold it upright, squirt some in until it stops seeping down, let it sit upright for a couple of minutes to work in, then turn it upside-down until the cleaner stops running out. Repeat until the cleaner coming out is the same colour as when it went in.
I believe on '99s the fuel filter is in the tank integral with the pump and must be replaced as a unit; only the '96-down XJs had the canister-type filter attached to the frame rail.
Check and clean the IAC first - it's an easy enough job. After cleaning it give it a few dozen miles to work out any loose crud that may not have come out with the cleaning and see if things improve.
