I know it doesn't work at the current size. But this site has the smallest banner of any board I'm on! haha And you could move the other ad banner to the right and save room that way.
Just resizing the banner a little bigger and no cropping the logo would be the best way to go IMO. Right now the site is very tight at the top anyway. Even without margins and padding the new graphic has some room to breathe as the PCB fades out.
The rainbow graph looked tacky, and making the PCB more visible will cut down on the legibility of the logo.
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