We just ordered a modular home. In the order sheet it specified for it have 3/4 " elevation under the cabinets and the doors to be prepped for hardwoods. The house came in today and NEITHER had been done. The cabinets are sitting right on the sub floor and from what I can tell the doors don't seem to be sitting any higher than they normally would be. The manufacter said that they will build us a new one to those specifications, but if we were to take this one they will knock 10% off the price. That's a BIG chunck of change. We have no idea what to do and have not been able to contact our installer. He was the one to told us to order it with those specifications, but I'm wondering how hard it would be for him to work around it and still do a quality job. Does anyone has any insight or advice on what to do?

It seems to me that as long as there would still be clearance for your dishwasher this should not be a problem. If there is not clearance for the dishwasher you would have to either remove your cabinet counter top and shim it up. Or modify your dishwasher. The issue at the doors is not a problem at all. At worst you would have to replace an exterior door. Though I would not expect that. Most likely you would install a different threshold, and trim the door off. If it is a metal door replacement might be necessary but not certainly.

If it were me I would take the discount. I would not expect any additional charges for your installer to work with the situation would come anywhere close to the 10% discount, and the end result should be undetectable.

Assuming it's post form top, I'd remove it and shim it up. Trim the 1.5" overhang out with some .5" stock and take the money to the bank. If it's granite dont touch it. You'll break it for sure.

I dont think there should be any signicant problems for your installer. Interior doors can be shortened without any difficulty, including the jamb sets.
Same with the kitchen cabinets, undercutting the gable ends and kickplates are a common occurance on re-fits to existing houses.
It is just a bit trickier on installation to avoid over surface nailing, but any competent installer should not have too much trouble with this installation.
Take the money and run

There are almost always options. If you can't undercut or shim the cabinets you can install a square nosing around them. Get them in plain wood and stain and finish them the same color as your floor. You can do the same with quarter round or trim of your choice but square nosing is better in my opinion. Still, having the cabinets sit on top is the best.

The doors can be trimmed easily.. unless they are metal in which case it wont be so easy. Good luck.