Tim,
I had mud flaps on my 91 E34 and while I wasn't crazy about the look, they served a purpose up here in New England. I think the mud flaps break up the natural lines of the E9 and since it's probably unlikely that the flaps will serve any real useful purpose, I'd have to say.....lose em.
(you really going to take that beautiful coupe up to ski-country or on some off-road rally?)
Then again, after looking at the pictures again, I'm guessing that you enjoy the outdoors (mountain bikes) and your Sierra-Nevada location lends itself to an occassional run to Kirkwood, so maybe the mudflaps are the way to go. I used to make an annual pilgrimage to K-wood and Squaw from Santa-Cruz with a '74 2002. Can't imagine attempting that in an E9.
I always thought the addition of certain fog lights on an E9 was really tasteful. I know the period-correct location differed from year-to-year, but I always thought that mounting the round Cibies inboard between the headlights and the kidney grill was the best location. I think that the later cars should have the rectangular lights to be correct (under the bumper)?, but regardless, I don't think anyone really gets offended if they end up above the bumper. I don't know what the standard operating procedure is for mounting fogs or driving lights above the big-bumpers, but if I had a big-bumper car and wanted to do things "my" way, I'd tuck them in a little closer to the grill so that if you're looking at the car from the side they don't protrude so much from the nose. .......and since you're asking, I'd humbly suggest that the size of the lights are a little large and aggressive for a car that is clearly not set up for rally duty. I mean, if you're going for that look, than you've got to commit and go all the way (lose the bumpers altogether, add white gumball number panels etc.)
Bottom line is I think your coupe looks fine w/o these things, but picturing the car w/ bikes or snowbards on the roof, steaming up Hwy 88 or 4.........it all makes perfect sense and would look pretty cool. You'd definately get a "thumbs-up" from me if I saw you on the road.