When you order your boot flashings, you must measure the interior diameter of the intended pipe to be flashed.
Most roofing and plumbing supply houses carry the lead in exact inch increments. The Oatey brand that I have seen only comes in 3" or 4", which are the most common ones needed.
Both the rigid rubber and the lead flashings just slide on the pipe.
If it is a PVC pipe and will have a smooth surface, the oatey rigid rubber ones will slide on smoothly. If you choose this type, trace a line aroun the pipe where the top portion of the flashing will be sealed to the pipe. Remove the flashing now and then install a high qualit sealant about a half inch higher than the traced line around the circumferance of the pipe. Do this when you are ready to install the flashing; ie. when you have the shingles installed up to that point. Then slide the flashing over the pipe and it will seal from the caulking slightly above the final resting position. Your rain shield idea is worthwhile, and they sell those at plumbing heating supply centers, but they are not a tight fit and will need to be caulked too, so why bother.
If it is a cast iron plumbing pipe, the beaded seam would slightly pust the rubber flashing away an prevent a completely tight seal.
When installing a lead flashing, they say to where gloves, so as not to have direct contact with the lead. You can tell that most of us roofers have not heeded that advice. Measure about 4" above the top of the pipe and GENTLY score the lead around the circumferance. Repeat lightly a second time if you barely scratched through the lead. Once it is scored sufficiently, you should be able to tear the lead along this line, or else keep using your stanley straight blade to score until it is completey through the lead.
Be careful. A slight slip can cut deeply with that sharp blade.
The Ice and water shield should only go on the left, right and top sides of the flashing. I would not apply caulk under the flashing flanges, but if you do, then DO NOT apply it under the bottom flange of the flashing, as any condensation from the pipe sweating would have no place to exit from and remain trapped under the flashing and eventually under the roofing materials.
This is way too Dang long of a response post for a pipe boot flashing instrruction!!!