I think you are going to need to use a hefty dose of "WiF-Zen" for this project. You made the right call scrapping the Anson. The land based Swordfish ... tougher call, but those weren't used all that much in the war - perhaps because it was pretty rare that any Axis targets were in range? They showed their worth from CVs for sure.
But keep in mind that the air counters don't always represent homogenous assemblies of several hundred aircraft of the exact same make and model, for one. I think most likely Bomber Command had some flying from all of the models present in the CW At-Start draw of 5 LND3 counters. Only hindsight and combat experience reveals the effectiveness of the aircraft design. But ultimately, just one LND3 is placed on the board.
Mapping the Battle of the Atlantic from history to WiF will also be pretty wonky no matter what you do. There are a whole lot of playability trade-offs in the Sub Combat system. Do you know what happened to the first UK aircraft that tried to sink a U-Boat? The U-Boat captured the air-crew.
You read that correctly. U-Boat 1, aircraft 0. The British bomber attempted to drop their bombs on a U-Boat discovered on the surface. The bombs bounced off the water and exploded in the air, causing the aircraft to wreck. The U-Boat chivalrously (still Sept. 1939) rescued the airmen and took them to a POW camp in Germany. It took the British until well in to 1940 to figure out how to sink U-Boats from the air - and when they did, short range aircraft were not the platform of choice at all. There were great rows between Bomber Command and Coastal Command (or perhaps Fleet Air Arm?) over who got four engine bombers coming off the assembly lines. The same happened with the Americans - conflicts that had to be settled by FDR himself (just like you in World in Flames - the Commander in Chief).
[Incidentally, on your next impulse you will need to get some U-Boats in to the North Sea so they can sink the HMS Courageous, or perhaps somewhere in the "Western Approaches", I forget.]
But for simplicity sake, aircraft vs SUBs are equally valuable in 1939 as any other year of the war, in WiF.
Another key - HEAVY CRUISERS WERE NOT ASW PLATFORMS. On many occasions, the Royal Navy would designate heavy surface ships to escort Convoys - when there was known to be a threat of a sortie of the Kriegsmarine. Even when this was done, the war ships maintained their own ASW escort of destroyers, and sailed at some distance to the actual convoy, because of the risk to the surface ships from submarines. Off Norway on the runs to Murmansk, the RN lost several heavy cruisers to the U-Boats. At a few other points in the war I believe, Cruisers were at time restricted from leaving port I believe, as their ASW escort had to be sent out with convoys as ASW assets were stretched to quite near the breaking point.
The Naval Combat system is a nice harmonious whole that can handle surface, air, and submarine interaction. But the playability comes at a decided price in the perceived realism of a Swordfish counter sortieing to the 0 box of the Bay of Biscay to heroically protect convoys inbound to England from the Africa route. Meanwhile, perhaps Heavy Cruisers in the 4 box get the jump on some Wolf-Packs with an excellent surprise roll and sink them all with their 8" guns, or perhaps a Battle Cruiser using it's 12-14" guns on the Surface Combat table.
The historical Germans built something like 1100 U-Boats from the 1930s to 1945, and lost about 700 of them, iirc (maybe 900?). At 15 per counter using Ships in Flames, 700 losses is 46 counters. Even at 30 per SUB, that's 21 SUBs sunk. Few games of WiF see that level of commitment with German SUBs.
My advice would be to use some of the "notional" ASW points given to Convoy Points in the newer rules, and also simply up those points considerably, and use the "input die roll" power to model the historical results. The Battle of the Atlantic was a long-term, attritional struggle for both sides, but in WiF, is modeled via the operational/tactical naval combat system. During the "Happy Time" and for quite a while afterwards, the U-Boats basically "find", in WiF parlance, every single turn, but I doubt there were very many historical turns where the Germans were able to take Combined impulses and simultaneously fight the Red Army.