It doesn't matter whether your node numbers are in the direction of flow. All the temperatures, etc. are usually assumed to be the same throughout the model.
If you want to renumber your model, open up the detailed spreadsheet by clicking the icon on the lower left, go to the elements page, highlight the rows that include the nodes you want to renumber, and then there's an icon on the right edge that starts the renumber dialog. You will have to go back through it to fix little things (sometimes restraint node numbers don't get changed, for example).
All of A234, A106B, and A105 have essentially (key word) the same properties, since they're all carbon steel. If I were doing analysis for a nuke, I would probably go to this much trouble, but for the real world this is generally not worth the bother. I doubt that it would change anything by more than a small fraction of one percent; the calculation methods aren't that good!
It's often a good idea to isolate fittings from pipe as you suggest, since in many systems different wall thicknesses are called out for fittings than for pipe. It also helps with keeping track of element boundaries so you can put supports far enough from weld lines.
Also, I am not sure, but I don't think the dimensional tolerances on fittings are the same as on the pipe. (Another one of those things not worth worrying about except in nuke-land.)
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CraigB