1 and 2
Either the roof, or the windows and doors should be done first. The roof is a standalone item, nothing tying into that scope of work, except for the gutters, but they are still not part of that work that will tie into the progress. I would not do the gutters until the siding is done.
The logic for the windows is, since you know what the various layers are before the siding goes on, the window can be grounded out with an 2X perimeter before the new windows go back in. That way when the insulation layer goes in the exterior window trim will be in the proper plane for the siding to finish against. I am assuming the Hardie plank is 3/8" thick, 2 layers at the laps and the ground set in the area where the old window trim resided, leaving enough beyond the existing siding to butt the new insulation layer against. The window will be nailed into this 2X, giving it a solid mounting. A jamb extension will need to go on the inside. The rip of 2X can be adjusted to flush up with the insulation layer if needed.
3 Decks
If the decks are to be attached to the house, the ledger needs to be weathered (flashing set) into the side of the house before the siding is run. The deck should be through bolted into the box sill (rim joist, some call it). If it is going to be freestanding then the deck can wait
4 and 5
Added plumbing and outlets. In case the existing siding needs to be violated to install any of the outlets, or perhaps the hose bibs, though most likely not, it is good to get the location for the bibs mapped, holes drilled, just to be sure there will be no issues after the siding goes on.
6 Siding
This will be the time to inspect the exterior and make any repairs before it is covered up with siding or covered by gutters. All electric additions will be done and accommodations are made for the extra hose bibs, though not yet installed. They could be installed, it would mean a lap at the bib. Otherwise a clean hole can be drilled through the siding if it is waited on.
If you choose to freestand the decks, now is the time to get those going.
7 Gutters
Sound fascia, siding done to mount downspouts to, job done.
As a point to consider, if you go with vinyl siding, choose a good brand, go the extra mile. I have Wolverine brand, 6" beaded, solid color all the way through, thick, resembles painted cedar. I built the house in 1989. The siding is 22 years old, with yearly power washing it looks great still. I have never washed the whole house, just touched up areas where gutters are, and algae grows (the biggest offender on shady spots only).
Another point, the nailing of the siding will be made really difficult trying to go through the Hardie siding, think about removing it.
Last item, the roof does not need to be done at first, but it is a major expense as is many of the projects you are planning. If it suits you, the roof could be done at the end as well, it would be a matter of being careful of the gutters. I would not do it at the end, I just want to make a point that there is no other items that directly impact that scope of work.
Best Answer
With Winter coming, it is a good idea to insulate around the pipe to prevent drafts, and possible freezing. Since I am assuming that this clean out protruding outside of the wall will eventually be removed, the methods for repair should be somewhat reversible so you can easily gain access to the pipe without having to cut back any more siding.
I would take a batt of fiberglass insulation, and cut off a few strips approx. 6" wide, and then peel off layers of the strips, dividing the thickness in half or thirds which makes it easy to work with. Then you can stuff the insulation pieces all around the pipe. You should add enough to fill the voids, and you can use a paint stirring stick, or a similar tool to pack it in. Be careful not to overly compress the insulation because it loses its thermal efficiency when packed too tightly.
After the insulation is put in, you can take some foam backer rod, and wrap it around the circumference of the pipe to fill the hole up to near the surface of the siding. The hole should also be waterproofed, so you should apply a layer of paintable exterior caulk over the backer rod to completely seal off the hole. You could then paint right over the caulk. If you are unsure what color paint to use, you can take a piece of the siding that was removed to a store that sells paint and have them match the color. Judging by the size of the hole, you would only need a small amount of paint. You can also paint right over the PVC pipe as well. I would also recommend using a good exterior primer since the paint would peel off easily if it wasn't primed. If you are looking for a more permanent solution, you can also use wood putty that is rated for outdoor use prior to painting to smooth it out even more.