Ok, after looking at those horribly rough pictures for a minute I couldn't stand it anymore and got after the cowl with the tinsnips. Using the lines in the sportster pad I made some marks on the cowl and started cutting.
My new #1 rule for working with fiberglass: Cut it before you cure it! This stuff trims easily a few minutes after it is hard enough to handle. Once it has cured it's like trying to cut sheetmetal, brittle, itchy, sheetmetal.
I think it looks a lot better now, but there is still more cutting and more layers to be added.
Here's the trimmed cowl on the seat pan:
Here's the tank's view of the seat pan, it gives a good idea of how much storage I'll have in there once it is complete. I'll have a removable pan on top of this pan that will be upholstered for the actual seat part.
And just for kicks, I slapped the sportster seat cover on my pan and laid the cowl on top of it:
More to come! This is cool stuff!