Most of the people that read these forums own their own kayaks or rafts, so responses may be slow. I have not used any of those companies in the way you ask about.
The closest I came was when some friends rafted 1/2 day Browns trip with Wilderness Aware Rafting and when I asked if I could tag along with my kayak they wanted $25. F#^& them. I just drove to the put-in and tagged along side my buddies anyway and hitched a ride at the take-out. (BTW, if a kayak takes out at their take-out, they want money for that too.
F#^& them. Other companies have had no problem and welcomed the "free" safety kayaker floating along the trip.
anyway, back at the farm.....
The prices you quote don't seem that high if it includes the hotel stays and a meal or three. If you were to just camp and run the sections in seperate day trips, it would probably be more money in the long run over 3 days. If it's that much money for 2 days, then you are probably better off doing the seperate trips thing.
Royal Gorge, Numbers, Browns, Parkdale. Those are the sections that offer the best exciting rides, in that order. The water level should be back down by mid-July that the Raft Companies will get back on the Royal Gorge, (less than 3400 cfs). Not sure about Numbers cut-off.
Everything else is sort of boring in the eyes of a older teenager or young adult, according to my four siblings and parents who have all rafted all these sections several times; one having been a raft guide. If the water is low, even Parkdale will be boring. ALL
Bighornsheep canyon above Parkdale is pretty mellow floating snooze fest with only the occational short class III-minus rapid. Just warning ya there.
I guess you allready picked up my opinion of Wilderness Aware Rafting.... I say go with (just about) anyone else. A smaller company will feel less like a "cattle drive."