Hi I'm installing new hardwood flooring throughout the upstairs of my house but I want to go room by room as I am renovating each room. As I am only laying floor room by room I believe I will need to install transition pieces perpendicular to my flooring under the jam using the same hardwood which is 5" wide. My questions are: has anyone done this before? Does it line up well? Should I just say screw it and redo all of the upstairs all at once?

Thanks

Depending on how long your project will be you could install a narrow rip that is left over from the last row of flooring that need to be cut to fit to the wall opposite the starting wall.
Planing a small chamfer on the edge with a block plane will prevent splinters.
The hall will be the most work, so doing it in the end after you get good at laying floor will help.
As long as you plan ahead, connecting all the rooms to the hall should not be a problem. You may want to purchase a bundle of narrow strips for the first row at the side of the hall you start on, or for ending against the other wall, assuming that you have a hall between the bedrooms. The flooring probably comes in different widths so you don't waste material cutting a wide plank when yopu only need a couple inches to finish up to a wall.

I did mine this way. Depending on which way the rooms are layed out some of the transitions will be parallel to the flooring in the room and some will be perpendicular. One of the benefits of perpendicular transitions is that they provide a stop/start point if you need to refinish just a room. If there is a central hallway that will be done last you will be doing what is referred to as net fitting which will take a little more time as you will be fitting rows that are boxed in on both ends by transitions. Also, if a room's boards and the hall's boards are both perpendicular to a transition, line up the boards so the joints on either side of the transition line up....this will give the best look.