removing the lesser monopolies? I not sure what you mean by that; removing the buildings or reducing their requirements? I think the real crux of the problem is strategic resources coming in 2-6 and being quite common, while the luxury chains (which I agree shouldn't be as common) comming in singles, sometimes in 2s. Granted, other buildings devour iron, coal and oil, and quite a few side buildings use horses, but it's a tough one.
For the record I play on huge maps, at the moment on very high resources, and have begun a very hungry campaign. It would have been possible to get an iron/horse monopoly from just my initial area+ the 5 city states who had been pouring resources into me. it probably would have meant i wouldn't have enough for foundries and such without conquest though. I've got to around 17 cities, biting holes in a couple of neighbours, and culture bombing city states whose land was resource rich (I still get the bonuses even if they are a 1 tile city!). I still don't have enough resources for a single monopoly, although I at 9 of silk and at 8 for a couple more. There are still two civs i've not found, so I'd estimate my land is around 1/3 of the map.
A comment; i've noticed that as you pull ahead in tech the number of great person's starts to get a little insane. Then again, you did say you hadn't balanced the upper end.
I'll start downloading this new version, may take half the night with my connection though. Any idea if it is savegame compatible?