Daniel, do you have a scale drawing of the basement with all the work you've done shown? Send it to me and I can mock up a benchwork layout.
I did this for Ed to make sure the dimensions of my yard would fit into his basement.
I can give you a scale diagram with key dimensions, like aisle widths, bench heights etc., as well as the 3-D views so you can visualize how it will fit around your water heater... should that be an issue!
I always start with the space I have available, position the highlighted scenes, then figure out how to connect the dots. On a large linear plan like yours, this shouldn't be too hard. If you think about it, that's how the 1:1 had to come up with their track plans!
Lee