From: Kansas, USA
To answer your questions, I looked at Scenario 3 from both sides.
1) I noticed that all of the Allied Aircraft at every Base airfield have experience in the 50s and every squadron has half their planes in "being repaired" status. The Jap Aircraft have experience in the 80s and every squadron fully operational. I also noted the number of Aces or Kills for each squadron.
Experience Levels of Pilots and total number of operational aircraft will greatly affect the outcome of any air to air battle, especially if they have a few Ace Pilots. The Allies are at an extreme disadvantage at the start of Scenario 3, with a lack of experience and plenty of damaged aircraft.
At Gili-Gili there are only 2 squadrons of Fighter-Bombers. Have 1 unit stand down for a turn with zero training, while the other unit is flying 50% CAP at 10000 feet. On the next turn reverse the assignments. This will help to repair some planes and also prevent pilot fatigue. If your pilots are always flying CAP, including in bad weather, their fatigue will shoot up to 60 or higher, and they will get shot down. Fatigue should not exceed 20 to 30 at maximum.
At Port Moresby you have 5 Fighter-bomber units available. You can set each unit to 30% CAP and also set their altitudes for each unit from 6000, 7000, 8000, 9000, 10000 feet. Most Jap Bombers arrive at 6000 feet and fighters at 8000 to 10K. Check the combat reports to verify their altitudes. Hopefully by spreading your CAP to different altitudes you can intercept a few fighters and bombers. Double check your pilots fatigue levels and also the number of aircraft available. If the ready aircraft fall below 6 then you need to completely stand down that unit until it can replenish enough planes to be effective. If their fatigue goes above 30, stand down to lower that number.
Do not transfer a unit of aircraft if there are damaged planes. Do not transfer a unit of aircraft if their fatigue is above 20. I would wait until all planes of that unit are completely repaired and pilots rested before transferring them out to another airfield. High damage and fatigue will result in additional non-combat aircraft losses.
2) Your Transport Task Forces moving into Port Moresby and Gili-Gili will attract every Jap Bomber if you place Minesweepers or any kind of Surface Combat Ship in the Task Force.
You can create a large task force at Brisbane to load the unit(s) that will be transported to Port Moresby. You should have that Task Force position itself about 10 hexes southwest from Port Moresby, then form several new task forces of 1 ship each. Move each single ship task force into Port Moresby over the next several turns.
There should NOT be more than 1 single ship task force docked in Port Moresby. When it is finished move the next single ship task force into Port. Timing is important so look at the operational point status and remaining troops / supplies left on the ship.
Most AP and AK ships of 1000 to 1500 load capacity will unload in about 1 or 2 turns. It will take about 3 turns for transport task forces, waiting on station, to move those 10 hexes, so you will need to spread them all out. You should also control the task force movement as it is leaving Port Moresby so it doesn't attract the bombers from Rabaul. Move them towards Townsville then let them move automatically back to Brisbane.
For those transports with 2000 or 3000 load capacity, keep them as a single ship task force. Use them to move the largest of land combat units like divisional units. If you have a divisional strength LCU that needs 4431 load capacity, form a task force of 3 AKs with 2000 capacity each for a total of 6000 load capacity. Get the whole unit to load and position the task force like all the other ones, then break it into single ship task forces. The large transport ships take several days to unload.
Use your CA, CL, and DD ships to form (3) Fast Transport Task Forces to move supplies and Base Force Engineers into Gili-Gili. Do NOT sacrifice your transports task forces at Gili-Gili, they are very slow and will get hit several times from Rabaul. The Fast Transports will move in and out during the night phase of the turn and they are very fast. From Brisabane to Gili-Gili to Brisbane in about 5 days.
3) Do not use your transport aircraft to move units that have heavy equipment.
Check your land combat units for the specific equipment that they have. If there are any mortars, anti-tank guns, or heavy AA guns your planes will not transport them, only the infantry, and all equipment will be fragmented units. Unit cohesiveness is important in defending Port Moresby and Gili-Gili.
I used every transport plane to airlift supplies from Cooktown to Port Moresby.
4) Your B-17s at Rockhampton can be used from Cooktown to bomb Buna, Lae, and Rabaul, but without fighter escort, they will be shot down. What I do is leave your bombers where they started. Set them to Stand down at zero training. This will keep them operational and accidental losses to the minimum. When the airfield at Cooktown is around 7 or 9 and your Bomber units are completely repaired and have available pilots for planes, transfer them to Cooktown.
When the airfield at Gili-Gili and Port Moresby is around 6+ you can transfer in a unit of bombers and a unit of fighters. Now plan your specific bombing missions from the front line bases. Remember that the fighters already located at Gili-Gili and Port Moresby are for CAP only, NOT escort missions.
When your bombers become fatigued, rotate the unit back to Cooktown and transfer another bomber unit to the front lines. Remember, do not transfer the unit if fatigue is above 20 and there are damaged planes. Stand down the unit for a couple of turns.
5) The Allied Player has 4 units of transport aircraft. I know that it only takes 3 units to move an HQ from Cooktown to Port Moresby, so sometimes the aircraft will transport supplies if the land combat unit has already been air lifted and the aircraft can still fly missions into Port Moresby.
Those Bombers that are stationed in Australia can be used effectively at Search Patrols. More importantly for Anti-Sub Warfare Search Patrols. You do not need surface combat ships to escort your transports if you have lots of aircraft performing that role. You can transfer the short range bombers to Cairns and Townsville, and that will cover the majority of Coral Sea for keeping enemy subs spotted.
Check your Base Force Engineer at Charter Towers. Once the Aircraft have been transferred to Cooktown, Cairns, and Townsville, you can move the Base Force Engineer to Townsville. Now use 2 APs with 1500 load capacity each, for 3000 total, to lift this Base Force unit to Port Moresby or Gili-Gili. Depends on your strategy to use heavy bomber from either base location. You will needs its aviation support to effectively plan bombing missions.
Another Unit is the Construction Battalion at Cooktown. It has 20 Engineering Vehicles. That means it can expand airfields and repair them really fast. Get this unit transferred to Port Moresby quickly. When your first transports from Brisbane unload at Port Moresby, have 2 or 3 transports return to Cooktown. Load the Construction Battalion Engineer unit and transport it to Port Moresby. Then have the transports return to Townsville and load the Base Force from Charter Towers to Port Moresby.
If you have any active aircraft remember to check the fatigue levels. IF it exceeds 30, stand down the squadron for a turn or two.