Also, another good reason to get a realtor is there are incentive programs you can get into... we used a realty program through Navy Federal Credit Union that gives a percentage back to you after you close. So, after we close on our home...we are going to get a check for 2k. The realtor is also nice in case the lender or the builder isn't doing something you like or not getting back to you... you can just call your realtor and say "sick-em!" and the realtor will whip them into shape. 
We also decided to purchase new... the nice part, for us, was the ability to save up for the down-payment. Our builder agreed to push our closing date to August and gave us extra closing cost money. We are using their preferred lender and they also gave us a lender credit. We got 15k in free upgrades and we are getting a free IPAD 2 as well. The builder also agreed to let us make payments on our earnest money deposit.
The other thing that we really liked was the ability to get a brand new house but then not having to get all the bells and whistles that jacks the price up. We plan on this being our only home (God willing) and decided that cosmetic things in the house we can always save and do later... so, we focused our upgrade money on structural upgrades that would be really hard to do ourselves. So, we got the X sq feet extensions on the house, the morning room addition, the alternate floor plan that gave us a master suite with a sitting room and put our laundry room upstairs - gas fireplace in the family room ... we also put a deck on the home... we opt'd to leave the basement unfinished and not take very many of the cosmetic upgrades. Luckily, a gourmet kitchen comes standard with our builder so that was nice. All in all, we ended up with a 3,600 sq ft home on almost 1 acre of land for less than 400k. Even our realtor was shocked that we were able to get that much home for 392k. Now.... we just have to wait... the waiting is the worst part.
In regards to upfront options... our builder only put the base price of the home and structural upgrades on our contract... they wait and do the options as an "addendum" after we pick them all out. They only require a small downpayment on the options and then that money gets rolled into our earnest money downpayment. They also give the choice of paying outright for any upgrades that we want. So, we could pick and choose what we wanted to pay for and what we wanted to roll into our loan. The crazy things that they charge you an "upgrade" fee for though is crazy.
Good luck though!
Sounds like the same plan that we had as well...do the structural upgrades and leave out the "easy" upgrades for later. For us, we go things like a bay window in the master and kitchen nook, convert dining room to a den, add an additional bedroom instead of a 3rd car garage, 8' interior doors, and paver driveway. Those are all things we felt would be pretty difficult to do later on. We did upgrade the kitchen with better cabinets/drawers and nicer granite, but only because it was it was so cheap to do now compared to what it would cost to do a whole new kitchen later. We did not get front or back landscaping, window coverings, interior paint (comes painted white) or any flooring updates...those are things we figured we can do as money permits...starting with window coverings first and the front landscaping second.