Whew! Have you been to an ear doctor? (I'm serious.) It seems very unlikely to me that your stereo caused this problem, but if I were you I'd certainly want to find out what did, and what I could do about it.
Your concern is not with "good" sound in the home, but with sound that is personally tolerable to you. If a boombox with the treble turned down can give you pain, an EQ may not help you much with your system. You need to get some auditory testing done. No one wants you to "turn your room into an anechoic chamber", and besides it seems as if you have already gone a long way towards that end. Attenuating the treble may do something, but it won't make your CD's sound like a live orchestra - the differences you heard have as much to do with the effects of mic'ing as they do with your system's balance or the CD medium.
To address your specific questions from above:
1) A parametric EQ will work fine on high frequencies. I think you may be misunderstanding what Rives is getting at with his description of his company's device. It sounds like a brilliant bit of applied engineering to me, but in any case not what you are after here. It is designed to deal with bass frequency room modes specifically.
2) Nothing is "bad" about graphic EQ for your application. In fact, a graphic model might well be the easiest thing to try out in order to satisfy your curiousity.
You are obviously not primarily concerned with "audiophile-approved" solutions, and besides it's not at all clear that there will even be a satisfactory solution to your dilemma. It would be easy to say, with the benefit of hindsight, that a B&W/Musical Fidelity system probably wasn't the best choice for your particular set of ears in your small room, but that's no guarantee you'd feel very much differently had you bought something like a tube electronics/electrostatic speaker system or a SET/small monitor system instead, or even purged your CD's and went all-analog. The devices you are looking at are relatively cheap, so buy one and do some experimenting if you like, but by all means get yourself to a specialist who might be able to help you with your fundamental auditory issue. Best of luck to you!