Honda recommends to change the Fuel pump at every 40,000kms. its in the owners manual. u shud get it changed now. u ll see the difference. this might be the issue due to which ur rpm is not going above 5000. but long ago, i THINK, someone told me theres a rev limiter in idsi vario too, that stops the rpm from going above 5000 when the car is parked but NOT when its being driven. so check for that too.
as for cvt, well, sounds are bad!! did u get original Honda cvt fluid in it? if no, thats the issue! if it is the cvt tranny issue, then the best bet would be to get it replaced. dont change the whole drive train. just the transmission.