I'm fixing up a old house and a standard steel entry door unit is too high.I can special order one but I have a 9 lite wooden door slab on hand from Lowe's so thought I might try my hand at making my own prehung.Once I have it made then set in place and install like any other.My rough opening I have framed at 34 1/2 inches wide.Now my plan is to make a box out of 1x6's at 34 inches wide.The door is a 32 inch door so this will leave a 1/4 inch space around all four sides of the door when set inside the box.The 32 plus half inch for space plus another inch and a half for the 1x6's gives me 34 with the other half inch being split both sides for the wedges.I believe so far everything is on the money just need someone to agree or correct me.Now when I place my door stops how close should they be to the door.I know may depend on the thickness of my weather stripping but how much should I be pressing into the weather stripping to get a good seal.Also what would be a good brand of hinges so that they hold up for years to come.Also if someone could point me to a good threshold to save having to rip this out later would be a help.I have never bought one so not really in the know as far as a quality one.

One way you can do this is mount the hinges to the door, then to the hinge side jamb. The hinges will mount 7" down from the top of the door. The lower hinges usually are mounted 11" up from the bottom of the door.
The hinges will need to be mortised into the jamb and the door, install your header jamb, then your lockset jamb. You should have 1/8' on all 3 sides (right, left & top if your opening is square). The bottom of the door you can cut to height as needed. Don't cut the jambs, they should be flush to the floor. Most of the time there will be a space between the top of the head jamb and the rough opening. (height R.O. of 82"-ish, door should be 80")
What I like to do as far as the door stops is I install the lock and strike plate, close the door, in the closed door position, then I install the stops.
Hinges I use Stanley. Threshold, whatever one works. Weather stripping, you can buy the rubber ones that nail onto the door stop or you can get door stop/weather stripping combo. Hope this helps.

Now as far as the jamb goes.Can I set my hinges right to the 2x4 of my rough opening or do I want to nail up say a 1x4 over this.Then mortise the hinges into the 1x4 and finish off the top and lock side the same way with 1x4 over the 2x4 to make up my jamb.

Go back to Lowe's and get a jamb kit. These are jambs to make your own "pre-hung" door. They should be in the door dept. or moulding area. Get the size you need for your door. You still need to mortise the hinges to the finished jamb (not the r.o. jamb) & door.