I'm far from an expert, but here's my 2¢...
My plan is to do the upper control arms first and setting them to stock lengths, Then install the new driveshafts and adjust the control arm accordingly to get a good pinion angle. Does this sound like a good plan?
You usually will make both upper and lower control arms longer than stock as your wheelbase will get shorter when you lift the vehicle. This will put the axles back to where they should be. I am waiting on my adjustable uppers, but will be setting the lowers to place the axles in the correct position, then adjusting the uppers to set pinion angles. If you doing just uppers then that will limit what you can adjust, which will just be the pinion angle, and not the axle position, but uppers are the best way to do that.
1.) I know the rear pinion angle needs to be adjusted, but does the front need it as well?
Yes, but the more you correct pinion angle, the worse caster will become, so you will have to find a compromise. I found that anything higher than 7.5º pinion angle will cause excessive vibration at the front. I'm currently around 6º with just under 4º caster (which is within spec). I plan on adjusting to about 5º caster once I get the uppers, maybe a little less if I can.
With only 3.5" of lift you should be able to get both pretty close.
2.) What is the proper angle I am looking for?
Here are the factory specs:
Good cancellation of U-joint operating angles is within 1º .
Operating angles less than 3º (U-joint system).
Operating angles less than 10º for constant velocity joint.
At least 1/2 of one degree continuous operating (propeller shaft) angle. On one U-joint system less than 1 1/2 degree operating angle.
With 4.5" of lift I could not get within the 3º but there is no vibration at below 7.5º, and you will be able to get much better than that.
Do not set pinion at 0º, as you want a little bit of angle to rotate the cups slightly so the grease gets moved around.
3.) Am I going to need a gear puller to change the flanges? ( the only articles I have found for a install is for the 1350's and I know you need to change the flanges.) Is this the case with the 1310 HD's?
Yes, you will be changing the flanges, I used 1310 OE's so didn't have to do that and can't help much. I think you will need to set the correct torque to rotate again, although if you measure it when pulling the flanges off it should be pretty easy to do. Although I suspect some people just torque them up tight. You should also replace the pinion nuts at least.
FWIW I replaced my UJ's with Spicer lifetime ones so I didn't have to worry about greasing them, as the ones on the double cardan were real hard to graese without pulling the shafts.