are the replacement doors larger than the doors your taking out the reason i ask this is you could leave the jambs up and just replace the doors
If your new doors aren't pre-hung you will have to make your own jambs. This is not for the faint of heart. You will need to measure on the hinge side of the door where your hinges will be located. You must match the jamb. You need to place the door on it's (doorknob) side. You can make 2 holders by placing a 2x4's on the floor (about three feet long) and nailing two 2x4's vertically to each side of the floor studs. This way here you can work comfortably with the door without trying to balance it on it's side while working on it. You may want to tack (preferably glue) carpeting or a soft material so you don't mar the door. They sell jigs that you tack to the side of the door that measures where you should be countersinking the hinges. You use the same measurements on the accepting wall jamb. You can outline the measurements with a pencil then carefully chisel out the wood. The hinges must be installed flush (same for the jamb) otherwise they will bind when you close the door. (You will need to make three of them.
You can do this without the jig but you need to be accurate in your measurements. They sell inexpensive homeowner - type jigs for a person like you who (maybe you can rent a good one) doesn't hang doors for a living. I suggest you look into it. Check with Home Depot or Lowes if there is one near you. Once you have your hinges installed on the door you will take the door and place it up against the jamb that will accept the hinges. You may want to keep the door from flailing about while you do this. Sometimes a piece of cardboard under the door will do. Make sure your hinge side jamb is securely fastened to the 2x4 behind it and that it is level (very important!).
Start with your top hinge (one screw only) then do the rest (only one screw in each hinge going into the jamb to start. Once the door is level, screw the rest of the hinge screws in. Check your door when swinging it to see if it will catch anywhere or if is nice and level at the top and latch side. You need to leave perhaps about a quarter inch gap around the door, especially on the latch side so that it moves freely. Open the door and install (tack) your latch receiving jamb to the 2x4 behind it. Only a finish nail should be used. Do not place the nail on the inside where the door will be closing as this will interfere with your testing of the alignment of the door. Once it looks good do not completely nail it to the 2x4 at this time as you still have a top (header) to install. You may not need to do anything at that point because most rough door openings are the same height.
If you need to install a horizontal header just open the door fully but look and see first if you need to install one and if you do, how far down it will need to come. You will be able to tell as you go along in the installation as you will see uneven spaces between the door and the jambs. The rest is cutting and finish nailing your trim. Start with the top of the door and go down each side. Most of the time the trim should rest on top of the baseboard trim. You need a miter box to cut your trim but don't worry if it's not perfect, that's what wood putty is for. Countersinking your nails and apply putty over them. Once the putty dries sand lightly flush, clean, and paint or stain. The most important part in hanging a door is the hinge side. Once that's installed and is right on the money, the rest is easy. This is one way to do it. You can also build your jamb around the door before you put it up against the door rough opening in the wall. I think I got everything you need to know but if not, let me know if you need further clarification.
Hope I Helped :)
You should leave 1/2" or less at the bottom of the door. If one room has a high pile carpet and the other has a bare finished wood floor you will need to consider the carpet side of the door. Take your 1/2" from there. You should not have more than an inch to an inch and a half gap in the rough opening. You can add a 2x4 at the header or sides if you see that you will be left with an inch or inch and a half gap once it's nailed. Another trick is to use a "1x4" pine board for your gap. These are actually 3/4 inches thick and will fill a gap if you see the gaps are too wide to handle the heavy door. Nail them solid against the header and sides of the opening.
You can then shim from that point. The 1/4" gap you mention is fine to work with. The 2" at the top is too much. Add a 1"x4" pine board as a 3/4" filler and that leaves you with an 1 1/4". You only need a nailer at the top header for the jamb anyway. There is no weight on the header. You just want to make it solid enough to accept a slammed heavy door without it moving. The most important is the hinge side. That is very crucial to your success in installing a nice level door. Make sure it isn't just level up and down you also need to make sure the hinge side door jamb is level from right to left.
In other words if your jamb sticks out 1/2" more to the right on the bottom and gradually levels off at the top of the jamb your door's bottom will hit the latch side first and you will not be able to close the door at all as the gap at the top of the latch jamb will have a gap equal to that 1/2". You don't want that. I would also suggest that you build the jamb one piece at a time starting with the hinge side. You could technically install just the hinge side jamb then hang your door on it before anything else is installed. If you did that you could actually see how much filler you need for the rest of the assembly.
It's easy to do it this way because you can always open the door to give you enough room to nail the header and latch side jambs. Running the door molding to the floor first is fine. Whatever looks clean. Like you said, it looks better that way in your case. A router is actually preferable to a chisel, that's what the jig does, it prevents you from going too deep. You may need the chisel to remove small specs of remaining wood chips. Thank you for the generous payment and bonus:)