I'm trying to dig up Xcal 45 tube amp picture to see how it looks.
You can specify the amorphous core version of most Lundahl output transformers for a hundred or so dollars more. It depends on the model, sometimes the cost increase is higher.
Between 2A3 and 45 my personal opinion is that it's better to focus on 45. The extra power from a 2A3 doesn't add anything for headphones in my experience. Also, even though a 2A3 is basically two 45 tubes in the same glass bottle, they don't really sound identical. My amp began life with the ability to use either tube. When it had its accident and had to be repaired I asked Glenn to remove the feature because I had a clear preference for the 45 sound and was never going to use the 2A3 mode.
There are definitely things I would do differently today. The choice of rectifier was probably the biggest one.
The big question is what is really the difference here between 45 and EL3N? Glenn feels the EL3N sounds as good as the 45. I'm sure the flavors are a little different, but both nice. I really would have liked to have the chance to compare the EL3N directly to my 45 so I could answer this question for myself and others, but that didn't come to pass.
There is also another possibility you might want to consider: basing your output stage around the 46 instead of the 45. I was very, very impressed with the 46 tubes I was sampling the other month. The most striking thing about them is the sense of air and space they put around the notes. The 45 has a very "dense" sound that doesn't really breathe a lot, and not everybody loves the intimacy of it. People talk about soundstage in terms of what "row" you are in....... well with the 45 you are literally in front of the microphone. The 46 throws a bigger sound field and lets everything out to breathe, and manages to have better resolution than the 45 tubes I compared it to as icing on the cake.
You can run the 46 with adapters even if you don't design the amp for it, but they end up getting run very hard that way and I think this tube is good enough that it might be worth designing the amp's operating points for it specifically. The major downside is there is no new production tubes available for the 46, and old stock is sometimes a pain to find.
