There are some good books on Ford EFI and OBD-II. Probably a simple google search for EEC-V (aka OBD-II Powertrain Control Module - PCM) will turn them up - I personally don't have any. Looked in my school library for some, and nada.
If you go with a bigger TB, you are going to want something to control air/fuel. Back in the prehistoric days before we discovered air/fuel controls that worked well, somebody dyno tested a bigger TB and lost power with the stock electronics. There are a few A/F controllers we use around here: Pro-M MAF Optimizer (analog controls at 2 throttle points), Apex-i S-AFC (digital control with interpolation), SHM MAFterburner (another digital one I know little about), Greddy e-manage (higher tech digital control that a CEGer has developed/is developing an add on to let us use its spark control). EEC Tuners have been on the verge of coming out with an application for us for a while it seems (would have spark control). Of course, there are chips as well: Diablo and Supechips. Can get off the shelf programs depending on your PCM code, or if you are lucky enough somebody local can dyno tune, which really is the best way to do it. MAF trickery (which is how many of the A/F controllers work) has its downside i.e. affects spark in ways you might not want it to.
A good start with bolt ons is an open intake, y pipe, and cat-back or better mufflers. Beware though, the stock y-pipe has a heat shield to keep the exhaust from heating the oil pan and we haven't really found a way to shield the oil pan well on aftermarket y pipes yet. Oil cooler is the best way to battle that, but it's a pretty involved installation for a good one.
The Duratec has a two piece intake manifold. What you see when you lift the hood is the upper intake, and below that is the lower which has the fuel rail and injectors attached to it as well as the Intake Manifold Runner Control. IMRC stays closed at low RPM for better low end torque and opens at high RPM (above ~3500-4000) for high end hp. The SVT upper is Extrude Honed from the factory, so it flows significantly better than the internally rough non-SVT. The SVT lower would have bigger ports than your 98 most likely. You'd need to use your current fuel rail and injectors as the later Duratecs (99+ or so) have a returnless fuel system, where the fuel pump controls pressure. Your 98 most likely has a vacuum regulated rising rate fuel pressure regulator. Not sure when the actual switch was made. The SVT lower also comes with larger capacity injectors (returnless use only), so it would throw the stock electronics off and throw a Check Engine Light (CEL) for running too rich, if for some reason you used them with a returnless system not set up for them.
I have a 3L (obviously) and I used all my SVT upper parts (heads, intake manifolds, etc.) with a 2001 Taurus Duratec 3L (VIN Code S - there is also a pushrod 3.0 in the Taurus), but the block required modification.
Here is a primer on all that. The 3L cams would work fine with a 98 Duratec, with one caveat. The 2.5 drives the water pump with a pulley running off one of the cams (intake I think?), and the 3.0 did not use the same WP drive until 2001. Also makes some 3L heads not compatible with a 2.5/3.0 swap, etc, etc. I forget if they actually are different cams; I think the exhaust cams have longer duration than the 2.5 exhaust cams but I'm not sure. bnoon and/or warmonger and/or Terry Haines might come along and give you the low down on that as I'm pretty sure they know. Maybe a search in the 3.0 Duratec or Performance forums) will bring up some of their old posts on this issue. We are pretty much SOL on aftermarket cams unless you got a junkyard set off a wrecked SVT (good luck parting an SVT motor!), but in reality the valvetrain setup won't handle much more aggressive of a grind anyway.
Phew! Hope this all helps. Welcome aboard. Read up - there is a lot of good info on here (don't forget the main page), depending on what you are looking for. If you need Ford OEM parts, but them from Bill Jenkins - most of us do. He works at a dealership in Las Vegas (just started this week at a new place, used to be in Boston) and we get a 25% or so discount. He also has a clue (unlike many Ford parts counters) and is an all around good guy.