I may be way off line here, because I don't have a good cad/cam program, but what I would do when I had finished modelling the whole part is to then divide it in two with a wall across where your 5 inch limit is. My turbo Cad program could do this so others should.
The wall can be the smallest thickness measurement your program can take, but should extend out from the main piece by a reasonable amount all round.
When your program then converts this to GCode it should do one side of the wall before climbing over and doing the other side.
If you insert an M1 in the code to stop the program, you can then move the part by a set amount.
As Brett says if you have some locating lugs on the part, you can then move it quite precisely.
Reset the DRO's on Mach 3 to the new location (i.e. 5 inches up from where you were) and let the program carry on.
The wall, if very thin, will either clean out easily, or break off in the general machining, particulary if you allow for the thickness whn moving the part.
I don't know whether this will work but I've read it over again and it sounds reasonable.