I have played around a little with this issue and would recommend a different approach as allied, especially for 1942 and into 1943. The main themes to me are:
1. Where are my fuel supplies?
2. Where do they need to go?
3. How do I get them there?
Question 1, the answer is simple: Los Angeles, Eastern US and Abadan.
Question 2, you need to supply Australian, Indian and to a much lesser extent New Zealand heavy industry with fuel. By doing this, you will generate piles supply from their heavy industry which you can then forward to support offensive operations. You need fleet fuel for Colombo and Pearl Harbor. You also need strategic stocks for offensive fleet operations in the South Pacific and East Indies. You need to select strategic bases that will become the logistic hubs for your early play as allied. When you select these hubs, you need to keep in mind how you will defend them if the Japanese come calling. My first moves have been to collect all the tankers in the East Indies in early December 1941, then load them with fuel and move them to Australian ports of interest, Darwin, Perth, Townsville and Brisbane. I do not send them back to the East Indies, once they are out they do not go back. Any competent Japanese human player will endeavor to block these routes and will target your tankers, so protect them and get them out of potential trouble.
Question 3, how? I send engineer and a naval base force to Christmas Island and set them to expand the port and airfield. While your East Indian tankers are making their trek, I collect all tankers on West Coast of the US to LA and and start sending a few tankers at a time with escort to Pearl and Christmas. I do not try to build intermediate fuel stores, but move the fuel to Australia. From LA, load up transport task forces with 4 - 5 tankers with a DD/PC escort and send them to Australia. Use waypoints. That is why you are developing Christmas Island. Create a task force, load it with fuel, send it to Brisbane (or Sydney) with "no refuel"and assign Christmas Island as the first waypoint with the refuel option set to "tactical", a second waypoint to a few hexes south of Pago Pago, and return trip set to "yes". This way, even 8,000 endurance tankers will be able to make the trip across the Pacific and make it back. The "continuous supply" option you mention merely automates the task force, ie it will run its mission and then repeat the same mission until you change it. This is fine, but especially early, I want maximum control over my tanker resources. In itself, it is not a strategic approach, but just saves you mouse clicks. As your target port expands, you can increase the size of these task forces and the amount of fuel they carry. Send a tanker group out once a week to minimize the risk of any Japanese raid crippling your tanker fleet, and over a couple of months you will have Australia swimming in fuel. You can use these a strategic stocks for New Guinea, Noumea or Darwin. The key is to keep your tankers well south of any Japanese raids and protected by intervening bases, Pago Pago, Souva, ect. If you try to use the small ports, you will have groups of tankers queuing to load or unload because the ports are just to small to transfer large amount of fuel even with naval support. At that point they are very vulnerable to raids, just as you described. As 1943 starts, you begin to get a flow of tankers and you can then build large fuel stockpiles anywhere you want.
I collect any tankers around India and send them to Abadan. I organize groups and send them to Colombo to support fleet operations and Karachi. You want to build ports and airfields in Karachi to exclude spoilage becoming an issue. From Karachi, you support Indian heavy industry and can move stocks to Perth if the Japanese player is attempting to interdict fuel from the West Coast US. Also, you can move fuel stocks from the East Coast US to Capetown to support Australia and India. You can you AKs to move fuel, I believe that they carry 1/2 their cargo capacity as fuel.
Net effect, it is in my opinion impossible for even the most aggressive Japanese player to interdict fuel flows to both the Eastern and Western Australia. You have flexibility and options for 1942, even when you are at your weakest. Your options only grow as 1943 and 1944 approach. All of this is just my method, you have any number of bases for potential hubs and multiple axes of advance to ponder.