My initial questions are:
1) Factors affecting the speed that a ship upgrade is completed (I imagine these factors would for the most part be the same as those impacting ship repair) including
This is the same as for repair. Bigger ports are better for bigger ships or can do lots of small ones. You have so many upgrades in April best just to start stuffing them in and let them get on with it. On the WC I found it was best to send the transport stuff returning over water to San Diego, the smaller of the ports, and leave the big three ports clear to deal with combat ships.
2) Is there any advantage to upgrading ships in separate ports - i.e. separating ships being repaired from ships for which only upgrades are being done?
Other than all the ships present will have a chance of using the shipyard points then no. I do think the number of ships in a port might affect repair rates, but this is just based on my experience. So I tend to clear a yard port of unimportant stuff, sending them to the nearest high port value bases.
3) Upgrading of individual ships be controlled manually rather than just have the game system automatically kick this off immediately when a ship becomes eligible for upgrading. Best method(s) for doing this if there are any? This would include such things as...
Obviously don't upgrade the Argonaut. But other than that, if a ship is going to be sat in a port, my philosophy is that it might as well be allowed to upgrade and repair some of the damage
4) Some time estimates or way of estimating how long a ship will take to upgrade (assuming the ship has no damage when it begins its upgrade)
BB's will gain about 4 sys for an upgrade but may take a month to clear it all. DD's will gain about 12 to 15 but will usually clear it in a few weeks. Note, your larger ships are still usable with this much damage but you really want to let the smaller ones repair before sending them back out.
Most of your subs upgrade as well. April is a minor upgrade, change of AA guns. But they all get a major upgrade in October, addition of radar. You have many many subs so start rotating your subs through the ports for upgrading so that they are all ready for the next upgrade in October. I usually upgrade them when they have to come in for some reason, but don't bring them in especially. You want to have them all kitted out with radar by January 43.
5) Did I leave something out....
Only that some of the larger ships need to be down to as low as 3 sys damage before they will upgrade so factor this into your plan if you have a well worn bombardment force coming in.