Im not a builder but a paint contractor.
In some cases the builder bids out the job as a complete,from all the subs bids.
Some contractors will show the bid of all their subs and others won't.
If you hired a builder that is when you should of gotten 3 bids from other builders (contractors)if you wanted to hire out all the work yourself then you should of called 3 plumbers,3 electricians,3 painters,3 drywall,3 roofers,etc..etc..and gotten all the bids from them individually,you can't go out and get your own subs now.This is why most people hire a contractor because he has all the people he uses in place.
As far as the windows unless it is in written on the bid form or quote he gave you saying that he will use those exact windows you want then he is pretty much able to use a good quality window of his choice.
No,just saying that you wanted these in a verbal agreement isn't enough,because there is no prrof of it even taken place.
I have a few contractors I do painting for and some I need to have everyhting written and signed because they like to change things on me.Other builders i do work for is just a handshake and a smile because I know that the work that I have and will be doing for them if anything changes they will folow up with my added price for the changes.
If you are strongly agreed to your terms then I would sit him down and let him know your feelings that it wasnt what you had wanted,if you let him push you around he will keep trying to do it.Either he is trying to save money or the siding guy's bid was below what he expected so he is using a lesser quality to get his profits up what ever the case may be.
Now as far as the length uit is taking him quite often different subs have different agendas or something happened to where 1 person messed up in the time frame.
Like example me I have been waiting 6 weeks to paint this 1 townhome but the drywaller messed up a few spots before he knew he did he moved onto another job now we are waiting for him to get back in their which in turn is going to make the time frame for the flooring,tile guy,carpet guy,cabinet person see it all falls in line.
The closing date on this is April 15th but it isn't even gonna be till about june 1st because now ive gotten onto another job because this one wasn't ready for me,but I will be thier when rockers are done.
Another example we just painted a home 3weeks ago and the heat some how messed up pipes froze and broke thus drywall is messed up and have to redone in 2 rooms.So things happen and your place is pretty good size,as long as you are seeing progress in the building you should be ok.
Alot of progress you can't see such as electricial,insulation,plumbing but it is still going on.
Well that was a long one,hopefully a little of this helped some.