I am going to reroof over shingles with metal on a house that has 4 valleys. What is the best way to Flash the valleys and end the metal panels at the valleys. How far should the flashing extend under the panels? Should I use modified roofing under the metal in the valleys. How should I attach the metal flashing, i.e. screws, nails?? I will be slatting the existing roof with treated 5/4 boards. What is the best way to cut the angle on the metal panels? I need all the help and info I can get.

Where ever your buying the metal roofing ask for valley flashing panels.
These are already made for valleys with the proper length to extend under the panels.
Use the proper screws that are made for the roofing your buying.

One way to cut the panels is with electric shears, there is also a panel cutter that looks like a huge paper cutter. Another way is install a plywood blade in a circular saw "backwards". (definitely were safety glasses with this one)

I have never heard of "valley flashing panels" and in fact when I do a Google search for them this page is the ONLY page that comes up...

The flashing valley panels he refers to is a formed panel with an inverted "V" in the middle. Sometimes called formed valley or "W" valley. It is standard to use it on metal roofs. On panels with lots of bends such as "U panels or M panels" we use friction blades for metal in a circular saw. Take your time and let the blade do the work. If you push the saw hard, you will burn up a blade before you get one sheet cut. Take your time and you can cut several panels with one blade. You can get the blades at any home improvement store, they are about $2.50 each.
Wade