I will have a much more detailed report later, but I am back now. Had a great trip. Trains in KL were all pretty good. Rode them along with some of the commuter stuff. Didn't end up riding the inner city stuff, because the bad weather on my first day messed up my plans.
Rode the train from Surabaya to Jakarta aboard the premier express train. Aside from being a little late right at the end of the journey I really enjoyed it. Trains were at least somewhat recently refurbished. Train was completely non smoking, which was a nice surprise compared to some of my other experiences in Southeast Asia. Train had a dining car where I had a lunch that was better then some meals I've eaten on Amtrak. Even though they appeared to only have a microwave to work with. Train averaged right around 60MPH the whole time. Stations were pretty decent, and there were some limited announcements in English.
I got fleeced by the taxi upon arriving in Jakarta. He refused to use the meter, so I guess I probably overpaid by like 3 dollars. Certainly not the end of the world, but its more the principal of the issue. I know Jakarta is a big city, but almost all the cab drivers I encountered didn't really know where they were going. Only after showing them my phone with Google Maps a couple times did I get where I needed to be. Uber was available, but I didn't try it.
Overall the train ride was pretty good, and if I ever found myself back in Indonesia I wouldn't hesitate to take a train somewhere. Although after spending a few days there in the biggest cities I don't think I would rush back. Didn't have the same energy as Vietnam a place I can't get enough of.