Alright, after extensive testing, here's my conclusion on how EXP works.
First and foremost, the only 2 things that influence EXP gained at the end of a song are the song's level, and the letter grade that corresponds with your accuracy (D, C, B, A, and S). There is no difference between regular S, silver S, and gold S as far as EXP is concerned. For example, clearing any level 10 song with an S rank will result in the play gaining 60 EXP, before any modifiers.
Secondly, both the DLC and Idol Buro give a 50% EXP bonus. If either are in effect, that 60 EXP from before now becomes 90. These bonuses stack, and are multiplicative. That means that if you play a song as Idol Buro with the DLC, you will receive 2.25x more EXP than normal. In the case of a decimal amount of EXP, it is rounded down to nearest whole number (55.5 would become just 55).
Third, Stage Challenges and In-Game Achievements give an extra 20 EXP regardless of any EXP multipliers. Daily Challenges give 20 or 30 EXP from the little bit of research I've done on them, but it seems like you only get 30 EXP challenges after playing the game for a while. On top of that, you will always get 3 20 EXP challenges when starting from a new file.
As far as allowing Daily Challenges in the run, I see no reason not to. You always start with 3, they all give 20 EXP, and it's incredibly unlikely the run goes on long enough to get another batch.
And I think that about sums up my research.
As far as EXP is concerned, I believe it has to do with song difficulty, accuracy, and any challenges completed. My guess is that the best way to level up would be to play through all songs on every difficulty, clearing as many challenges as possible in as few clears as possible. For the majority of songs, at least the ones I looked at, it should be possible to get all challenges in a single clear. One of the exceptions is Shenri Kuaira -repeat- since you need to get hit 19 or more times and get 8 or fewer misses.
I'll get started on a route if you haven't already. I think this will make for a really interesting category that makes the speedruns more than just menuing.