There are probably hours of posts about this subject scattered among the forums.
Put simply, the SW99 is a P99 made using a S&W slide & barrel. By that I mean that Walther made the frame (with some minor cosmetic and ergonomics changes requested by S&W) and provided the same parts for assembly of the frame and slide that are used in the P99. Only the bare slide and barrel were made by S&W. The rest are the same Walther parts used in the Walther models.
S&W engineers helped to finally identify the "early slide stop" issues that affected both the P9940 & the SW9940 in the early years. Walther took the info and had Mec-Gar redesign the .40 S&W magazine body & follower. (S&W also requested a heavier slide stop spring at one point, but it didn't completely resolve the issue.)
A couple of the changes requested by S&W for the SW99 frames were eventually adopted in the P99 series, such as the elimination of the hooked frame tang (which pressed down into the web of the shooter's hands), and the more universal accessory rail).
Personally, I liked how the S&W barrels were revised during production to incorporate a machined flat spot on the bottom, toward the rear, where the recoil spring would rub during unlocking/locking. The barrels also received some different finishing in the way of chamber mouths/feedramps, barrel tabs, muzzle crowns, etc as SW99 production continued.
Walther continued to revise and refine their 99 design. Some changes were easily noticed ... trigger guard, frame ergos, slide contours, mag catch levers, etc. Some of the continuing refinements and improvements aren't easily visible, especially inside the frame ... such as the dimensions of the frame where the sear housing is seated and the replacement of the small steel post used as the trigger bar guide (in the bottom of the sear housing block) with an adjustable steel lever.
This shows some early and later revised sear housing blocks, where you can see the difference in the length of the hollow tube/pin. (There's been a further revision replacing the steel post used as the trigger bar guide with a lever, though.)
Overall, the 99 series is a pretty good service-type pistol.
I've been an owner & users for several years, as well as an armorer (3 classes/recerts, including one where the armorer manual showed the weird configuration demanded by the NJSP, called the SW99NJ - there's a longer story about that gun, but this isn't the thread for it).
I carried one for a few years and helped support about 50+ SW99's for some time, both issued and personally-owned. I know of some SW99's that have seen several thousand rounds fired, and a couple which have seen more than 60K rounds fired. I've fired many thousands of rounds through various models, including over 12K rounds through my own SW999c (9mm compact with the AS mode sear housing block).
As an armorer I've repaired both SW99 & P99 pistols.
I always felt the 99 series never received the appreciation it deserved in this country, but then there were a number of other plastic pistols which were competing with it, and at a lower price point. It probably didn't help that Walther didn't ship as many units here as potential owners might have wished, but at one point I was told by someone at Walther America that Walther was focusing a lot of its attention on its international sales. Pistols and parts were sent here on a schedule of Walther's devising.
BTW, as long as the used SW9940 you bought has the revised mag bodies, they ought to be fine. You can still order springs (and followers) from S&W's Walther America business. (The agreement between S&W and Walther expires in 2013, although I imagine S&W will continue to carry some basic parts due to their limited lifetime warranty support - to the original owner - of the SW99 & SW990L models.)
This image shows the revised mag body (left) and the original one (right). You want the ones on the left. In the P99's the followers were different shades of light blue as the followers were revised.
Personally, I always tended to favor the 99 series chambered in 9mm (much as I do the Glock).
The triggers seem to become a bit lighter & smooth as the guns are used. The standard sear mode (what Walther presently calls the Anti-Stress/AS) is my personal favorite, although some folks claim to prefer the Quick Action/QA (the SW990L used the QA sear block, but S&W didn't use a slide with the reduced size field-stripping button like Walther used in their QA models).
I've never come across a P990 (what Walther presently calls the P99 DAO), which was a true DAO configuration.
Don't try to detail/armorer strip the frame. The locking block pin is pressed into place with a press (although armorers are taught how to remove it with a roll pin punch and ball peen hammer). The only time it really has to be removed is if a slide stop spring has to be replaced. Take care not to snag the rear end of the slide stop spring during cleaning. (S&W finally sent some Walther closed loop slide stop springs to at least one agency, because some of their people didn't seem able to stop themselves from snagging & bending the springs.
The Walther spring has a shorter, closed loop end, while the spring made for the S&W models is longer and has a hooked end (which you can see above the rear of the slide stop lever tab).
There are some other little tips to keep in mind to avoid damaging the 99's when performing armorer level inspections & repairs, too.
The sear housing block is NOT an assembly intended for armorer level disassembly & service, although armorers used to be told how to replace one spring & lever (which could disassemble itself during shipping of a replacement sear housing block
Also, nowadays the striker assembly isn't considered something armorers should disassemble.
I happen to like the way the extractor can be removed and serviced/cleaned) independent of the striker assembly being removed from the slide, although some care must be used when reinstalling the 2 plungers & springs.
Congrats. Enjoy the SW9940.