Is the rear of the running board bolted to the front of the rear fender? Is the running board also sitting mostly level front to back?
If the answers are both yes, all you need to do is man handle the curved splash panels until they close that gap between the splash panel and the bottom of the bed.
I just went through this same scenario on a $55,000 + build for a guy. All new running boards, splash panels, and running board brackets.
I installed the brackets with 5/16" stainless steel nuts, bolts and lock washers and left the bolts loosey goosey.
I then laid the running boards on the bracket and fished all of the running board bolts in the bracket holes and tightened the nuts just to take out the slack.
I then tightened the bracket-to-frame bolts all the way, and then tightened the running board nuts.
I then installed the too-short curved splash pans to see how much I needed to take out of the curve to make them taller, removed them, man handled them and reinstalled. Work fine. Last long time.
