I wonder does anyone really know what MoCo did to these motors? I've heard some say (as quoted above) that they came with Stage I kits, but I know mine did not. ... I have also heard things ranging from "performance cam" to "bored over" - but fact is, I don't think so.
I have a sales brochure for my FXR2 as well as the owner's manual. There's nothing in either that would indicate that the motors are anything but a stock Evo. The sales brochure lists all kinds of features, so I would think that if any motor upgrades were present from the factory, they would certainly be listed there. The bore/stroke is listed (stock Evo) as well as displacement (stock Evo again). They state the torque as 76 ft-lbs, however, which sounds a bit optimistic for a stock Evo, but I could be wrong. Have to dig around for the same spec for other 1999 Evo motors for comparison. All that having been said, it wouldn't surprise me to find that Stage 1 kits were installed at dealers as near standard procedure on most or all of these bikes.
As for Stage 1 kits on FXR4's, well, surf ebay for a fXR4 brochure and see if it says anything. Again, I think if HD did it at the factory, they'd have it in the brochure.
When I had my heads, ignition and cam installed, the difference over stock was very noticeable, even though I've never had it on a dyno, so I can testify as to the upgrade from stock that those parts provided. So, unless somebody's got some good information otherwise, I'm going to stick with the opinion of the factory installing stock Evos on CVO FXR's
The EVO has a distinctive sound, and side-by-side with my '05 Dyna Low Rider (TC88) with similar pipes - the EVO is significantly louder.
My motor took on a different tone after the mods. "Crisper" for lack of a better term. Not sure if it's any louder, but it is different.