Does it make more sense to put the ridge on top of the v.b. and nail the ridge to the v.b.? **** The ridge is easier to figure placement by putting in first. The simplest way is string a line over the common rafter tops at the peak from about 15' back away from the old roof. Mark the spot, clean the old roof there, check it again, mark it. Drive a nail there with head sticking up 1".
Put end of chalk line hook on nail, go to the intersecting of old roof/valley. Put a straight-edge or string across rafters as ply would lay (right angle to rafters) and mark where it hits old roof. Remove old roofing there and a little above. Snap the chalk line on old roofing for valley outline. Remove roofing there and other side for valley, 2'-3' slot. Re-snap chalk on old sheathing.
While at old roof/new valley line, lay a short 2x (1-1/2") next to the line, but lower down the old roof and under the straight edge. This is to allow for the valley material thickness and still have the tops level with the common rafters plane. 2-3" lower from the line snapped for valley to keep planes level. If you installed v.r. on the first line it would be higher than the commons by 1-1/2" vertically. Snap a new line parallel to first line for the top edge of valley board. (Dropping the valley it's thickness).
Install the ridge to the shorter apex lines, not the first line. Layout ridge from last common starting there. Install valley boards, in pieces if needed, break joint on house rafters. Check last common for straightness, or use 2nd common back. Hook tape measure on common, across the roof as ply lies, and mark layout of next valley jack on top edge of valley board. Move tape-m up about 2-1/2' and mark second v.jack, which will be 24" farther on tape-m. Then simply measure length of v.jacks and write it on ridge side, big- so read from ground. Remember as cutting if short point or long. Cut shorter (opposite sides) jacks from waste of longer jacks. Always cut heels in center of boards, to use the waste heel for opposite side, shorter jack.
After installing jacks with full support under by valley boards, install a 2x6 under the ridge, flat, sitting on v.b.'s for ridge support. Install 1x4's at every pair of jacks, to tie opposites.
Sheath commons in stair-step pattern, as many full sheets as possible, right to the ridge, starting from end away from valleys. Then sheath over the valleys, using the first caulk line for measurements. I find it way easier to fill in the valley sheathing starting with the ridge ply first. Always write the measurement of the width first, like in window sizes, so not to get confused. eg. Square right, 54"x7-1/4" = Ply is 48" on right side (up and down the rafter), 54" across the top (8'way), and 7-1/4" across the bottom (8'way). Your strength grain of ply or osb will never get installed wrong.
The 3" is ply nailing, along the valley board and along the old roof sheathing. The v.b.'s just nail 3-16d's into old rafters every time they cross over one.
Be safe, G