Something to consider with the "SR5 Wides" is that the sheet metal is drilled in order for the flares to be anchored on. This is not the case with the "skinny blacks" I believe.
Also, with the black flares, I think there are OEM front mud flaps available since you don't like the unfinished look (don't blame you) when the step rails are removed.
Firstly there are four different flares that came on the third gen
Limited Flares: Came on limited's 1996-2002
These always came with the side cladding, and its built into the door part of the rear flare. I think the mudflap of the rear flare is different than the sport flares. Also these always had the running boards. They mount using clips that fit into holes that are on the body. not exactly sure but from 1996-1999 these only came in two colors, silver and dark grey (maybe black), from 2000-2002 they came in various colors
SR5 Skinny Black: Came on SR5, always on 99 highlander 1996-2000
Other than the Highlanders these were a dealer only add on. When these didnt come with running boards they had a special front mudflap thats really rare and sought after. They mount using holes in the fender lip the same as the chrome strips.
SR5 Wide/ Sport: 2000-2002 SR5 and always on the Sport Edition
These are just like the Limited flares but have a different rear mudflap and there is no cladding on the doors.
Skinny Chrome: 1996-2002 sr5 and base.
i dont think there are mud flaps available for the limited or sport flares, and I had to drill holes under the lip of the fender well for my skinny black flares, but mine came with no flares at all not even the chrome strips.
Honestly I dont think anyone has ever put the wide sr5 flares on a 4runner that didnt come with one. First you will need to drill some square holes for them, and in a pretty accurate pattern, could be quite the project. if you do this, id try to make some templates based on someone elses that came with them, they would have to remove them so you could get the pattern, and i think the clips usually break when they are removed, so unless youve got a good friend with a 4runner i dont think anyone will let you take their flares off and see what it looks like. you might be able to figure out the pattern just using the flare but it would be a lot easier to use a big piece of paper on the body of the truck and mark the holes.
Anyways good luck with the flares.