I do add in an infused pump, but didn't add pipes/tanks.
I was on the fence about those as I want to limit which things get an infused version. Thinking about it more, and how high the throughput of the refinery and chemical plant is going to be when moduled, I think it makes sense to have infused pipes/tanks.
Other tempting bits to have upgraded versions are refined concrete, stack & stack filter inserter, and maybe steel chest. I have a feeling refined concrete would look really cool. The inserters may be necessary to keep moduled assemblers appropriately fed.
Trains I think I will leave alone, unless they really need a buff. Definitely need to play test this, but I am happy with how it is coming along so far!