i just took a good long look at the same parts on my 8E. the left side(driver side) screw head just nearly touches the upper deck. the other side has 1/8 inch of clearance. my screws and parts looks the same as in your pics.
maybe your blue metal bell crank(the thing the steering links bolt to) isnt sitting right? if its up to much it could cause your problem.

even tho 1 of my screws touches the upper deck, its not nearly enough to cause an issue. in one of your pics it looks like you already trimmed some of the upper deck to get more clearance?