Crown Boiler Piping Question

I have been in my house for approximately 3 years. I noticed issues with the Crown, Series 32, boiler but didn't know the extent of the problems until 2 years in. I don't know how old the Crown boiler that was replaced was and incorrectly thought that it would be original for the house. Upon closer inspection I found multiple holes in the tops of the cast boiler sections leaking water and steam. It was time to replace the unit. I contacted a couple of local companies that specialized in steam heat but none wanted to take on the project. One suggestion was to simply replace the Crown boiler sections with new sections. With a call to Crown/Velocity, which had the sections in stock, I decided to replace the 6 sections myself.

After install, and a second replacement of a bad cast section, the system was up and running last season. My hope was that the original system of piping would work correctly if only the boiler was replaced with an identical system. I dealt with the surge and skimming last season but found that, when the temperatures were cold enough to have the boiler cycling quickly, the water would disappear in the sight glass. I am assuming there is a vacuum situation somewhere in the system. And that the holes in the old boiler masked the problems?

One concern I have relates to the 3 inch header pipe required in the Crown install manual. After installing the boiler, I started to question the header piping that was already part of the system. The header starts at 3 inches, is reduced to 2 inches and then increased to 4 inches. Pictures attached. I have read a number of books on steam heat and have seen some issues about the water disappearing in the sight glass being addressed in the blog.

Are there any thoughts on the 3" down to 2" and back up to 4" on the header piping that may be a problem?