I'm not sure what to tell you about cleaning the marks you already have but to prevent future markings use some old t-shirts / towels and drape them over where your tire contacts the interior trim. Works great!
that's a pretty cool setup e_biker.
on second thought you might want to try using Tuff Stuff - a readily available carpet cleaner that's usually for sale at automotive stores, wally worlds, etc. Spray some of that on the spot, scrub with a brush, and wipe clean.
For general interior cleanup i use a wet rag sometimes spray a little soapy water on the hard surfaces. On the dash and steering wheel I like to shoot a spray of CRL Plastic Cleaner - it's very close to Plexus but half the price.. and it DOES NOT leave streaks or fade the dash.
That photo really helps me !Agreed, tire marks are a pain to remove. I designed a tray that holds two bikes but you have to take the front wheel off each bike to mount them in the E. This way you can even keep one rear seat in and functioning if you want.
I loaded my bikes "wheels on" and ran into the same issue you are. Good old 409 is finally what took off the marks on the plastics. Side and rear pic of the bikes loaded. Here is the clamp that I have on either end of the box to clamp to the fork. It's been in use for a little more than a year, no problems. Here is the original post.