New RVer with some diesel fuel issues.

I bought a diesel pusher 2 months ago. The day I bought it I had the oil and fuel filters changed. Took first long trip last week. All was going great that I started having issues. It initially felt like transmission issues. I was getting check engine light and had no power. Started wondering about fuel. I limped to the gas station. I filled it up. I seemed to have full power after. I left. An hour later, it came back. I kept going because engine gauges were fine. It self corrected. I made it to our site. I started researching and learned about diesel and algae. I purchased some treatment and put in the tank. The morning we left, I went straight to a Loves’s. I had them drain the bottom of the tank a bit. Didn’t see anything bad come out. I had them replace the fuel filter and the fuel/water separated. There was not an additional filter as some point out. These filters were only a month old with about 200 miles on them. The fuel water separator has some black chunks. I left, 1 hour in it started again. I was right at an exit and stopped at Loves to try and read the check engine light. Their pc said there were codes but the database was not able to identify it. I put fuel in with the appropriate mix of treatment. I left, and couldn’t even get out of the lot faster than 15mph. I was driving down the road trying to figure out where to turn around and it just went away. I decided to get on the road. I drove 6 hours without an issue. Came home, unpacked and took it to storage. On the way up it started again. It didn’t go away before I arrived but the other three times it self corrected. I decided to run a camera into the tank and look. Before even getting to the tank, I found the filler necks are totally disgusting. Now I am not even sure what to do next. Do I replace the necks or can they be cleaned. If the fillers are bad, what about the tank and other hoses. Not even sure what to do now. Made appointment with Freightliner, but can’t get in for over a month.