Some good advice thus far. I'm a fairly new player myself, though I've had Uncommon Valor for a few years. I would recommend starting with the tutorial scenario, which is loosely based on the Marianas Turkey Shoot. There is a tutorial manual that will step you through the first couple of turns. I played that first and it took me about 10 days to complete it.
The rest of my suggestions are for the full campaign.
ORIGINAL: Greyeye
1. What are the best bases to start supply runs from?
On the West Coast, I run most of my supply out of SF and fuel out of Los Angeles. I've tried both transhipping supplies to Pearl and distributing from there and sending direct from the West Coast. I've settled on direct shipments. Overall, I don't think there is much difference in the long run. I do have a large cache of supplies at Pearl for the Central Pacific bases, but most everything else goes direct from the West Coast.
2. What is the most important thing to bring from the US into my island bases in the central and south pacific (supplies or oil)?
Oil is only used at industrial bases where it is converted to fuel. Fuel is only used by ships. Avgas is lumped in with supplies. You need enough fuel at bases that have ships based at them so you can continue operations without problems. I have some fuel at most of my bases to refuel long haul cargo ships on their return journeys. The bulk of my fuel is at bases where my fleets are.
Every base needs supply. If you check the master base screen (star or meatball icon on the top bar), you will see bases running low on supplies will show up as orange in the supply collumn. Bases running out of supplies will be red.
3. In the first turn the japanese have landed troops on Wake....Do I have a chance to hold there?
I experimented running the first turn 5 or 6 times and Wake fell on December 7 every time. I've never heard of Wake holding out more than a day or two. If you're playing against the AI, Wake makes a good place to train your carrier pilots. After the first week or two of the game, the AI will leave a couple of units at Wake and start focusing forces in the islands south of Japan. I sent carrier task forces to Wake a few times to get bombing practice. The carriers are parked off Wake for a few days and they pound the place flat, then return to Pearl.
4. Are AKs the best way to get all those planes over from the US?
Often it will be the only way. If you want to transfer aircraft based in the West Coast, you will have to transfer them to another headquarter burning political points. Early in the game, you won't have many bases capable of operating larger bombers, so you are best off leaving most of them in the US until you get some bases built up. There is a formula for how big a base needs to be for a bomber to operate most efficiently. It's based on the maximum load of the plane.
Depending on whether you're playing the stock game or one of the variants, B-17s require a size 5 or 6 base. Most medium bombers require a size 4 base.
You will need to ship your engineers around to get the bases built up. When I started my game against the AI, I marched the engineers in Malaya down to Singapore and moved them to bases further back in the Dutch East Indies to get some more defendable bases built up.
I'm in August 1942 now and I still have a fair number of units in the West Coast of the US. AKs are probably what you will need to use for the shorter range aircraft. B-24s can make the flight from the West Coast to Hawaii in one shot. As others have said, you can use carriers too. Later in the game, you will get some aircraft ferry CVEs which come with no airgroup. These are a good way of moving single engine and some twin engine aircraft without have to have the aircraft damaged and repaired with transit. Until you get these, you will either have to use fleet carriers for this, or AKs. The fleet carriers are too valuable and are the only thing you have to counter the Japanese carriers effectively, so you will be using AKs for most aircraft transports.
5. Where is the best place to send all my subs? Or are they so useless with crappy torpedoes that they are more recon assets?
The US long range subs are not as useful the first year of the war. One thing that will improve sub effectiveness is to replace the commanders with more aggressive captains. To change the sub captain, you need to select the sub within the task force (even if only one sub) and replace him there. If you replace the commander from the task force screen, you will only replace the commander of the mission and the sub will still have the same captain. You then have to disband the task force and reform it to get the new commander as commander of the task force as well as the sub. If you have a bunch of subs in a port, you can form a task force with all of them, change all the commanders, then disband it.
The US starts out with some extremely passive sub captains and that will greatly affect whether they attack or not. When I started replacing captains, I started seeing a lot more sub attacks. The long range subs still don't get many hits, but the S class subs do get hits when they attack. The Dutch and British subs also get results.
Another sub mission which can give the Japanese fits is mine laying in their ports. The US long range subs are probably more useful for mine laying of emergency transports in the first year of the war. I have most of mine possitioned off the coast of Japan though. With agressive commanders, they do make a lot of attacks in a target rich environment. One of them put a torpedo into the Akagi doing some serious damage. I later was able to sink her while transfering to another base for repairs.
6. Can someone give me a quick rundown on plane upgrades and how that occurs?
There is an option for doing player defined upgrades (PDU), which allows you to set which plane a unit will switch to. With the option turned off, the unit will upgrade along a predetermined upgrade path.
When a unit is at a base with more than 20K supply, or within some distance (a few hexes, I forget the exact criteria), and there is enough aircraft of the new type in the pool, the unit will upgrade to the new plane type. All of the new aircraft will be set to damaged and it will usually take a couple of days to get the unit back to full strength. When I was doing a lot of upgrades, I had a couple of bases behind the lines I sent planes to for upgrading. That way they aren't subject to combat while their new planes are being brought up to combat readiness.
7. Can I build forts at locations that are not bases?
I see someone else answered this one.
Bill