Dealer markup has always been high anywhere -- standard is around 1500 for warranty, 1,000 lojack, tire protection 100-400 (depends on what the coverage is). I don't know about IBEX, but overall I don't think they're charging twice what another dealer would.
If you're only a few months away, wait... otherwise you're spending $3k to get a car that much sooner. Is it worth an extra $1k/mo ? Probably not... so yes, waiting is better. You'll probably end up getting the warranty though... 24 months isn't that great and is geared towards people willing to service their cars themselves in 25 months. I got the 60 month warranty.
Definitely save for that down payment... a grand will help your financing terms. And pay down credit cards a month before if possible, to raise your credit score. Mine went up 150 points in a month by doing just that.