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Welcome to the forum, Steve. It's been a loooong time since I fooled with a servicar but I believe that your side to side misalignment is caused because the rear end has been flipped over to accommodate the left side pan head chain drive. The WL's have the drive chain on the right side. I believe that if you measure the frog legs you will find that they are more offset to the right. Part of this is due to the original location of the brake master cylinder and chain on the right side. The drive chain dilemma might be easily solved with a jackshaft solution to move the chain left to right. There should be room in the frame with no centered rear wheel. the jackshaft solution would also provide a gear ratio solution for better highway performance.
The braces on the rear end are designed to be in tension and were originally located on the bottom. They don't provide much strength in compression as they are now. With the rear flipped you are running everything bckwards. Don't think that is a problem but check you brake shoes. There is normally a primary and secondary shoe on a drum brake system for maximum performance. Running them backwards on a flipped rear end might further decrease their effectiveness.
If you look at the original WL frame you will notice that the engine and trans mount in a lower saddle so the rear axle is in effect higher. I would agree that the rear frame section has to move up on your setup.
I might have a suggestion for the disk brake setup but have to do some research first.
Looking forward to more build pix.
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