Sorry, I was only mentioning that because my problem was originally about the winches until I realized it was also the ports. I uninstalled most of my mods, now all I have installed are KIS, KAS, and Planetary Base Mods. Tested it again and same problem, although I am testing the ports on Planetary Base parts. I also deleted and redownloaded KAS and KIS then applied the KAS patch, one thing I noticed when reinstalling them was my game prompted me and asked if I wanted to allow them to check for updates and I clicked 'yes'. Do you suppose this could be part of the problem? Anyway here is a screenshot of my error log. In the mean time I am gonna test the parts on some stock parts and get back to you.
http://imgur.com/HuifWH2