Bobby
I leave enough space behind to either send the kiddo with a rake and wheelbarrow or I can just pull behind with a frontend loader and rake scoop and go. I treated my floor boards with thompsons and pee and poop shoots off with no problems.
I will say I prefer all wood vs metal. If you don't know why put several male dogs in an all metal one for a few years and find out. The drawbacks are hot in summer and cold in winter. But so far the good far exceeds the bad. Coupled with my larger day run type pens they are awesome.
I have 3 runs built on concrete, but I used treated lumber and chainlink fence for the same pee problems you mentioned.
I believe I will build a set for my crop of pups and expand from there.