I'm thinking of doing the following for ver 1.1: mapping left shot, right shot, option, and power up to the four buttons. Then when I get to one of the bosses in chapter 4, pause the game, change the option button to the bomb button, and continue like that. Thankfully they let you change the buttons on the fly, so you can pause it whenever and swap them. This is the only reasonable solution I can think of for ver 1.1 with an Otomedius stick.
Also, I tested this on my RGB monitor. For those wondering how Arcade mode looks, well, it is interlaced, so it looks like any other interlaced originally 240p game on an RGB monitor. It is not blurry like the Mushi or Ibara ports (thank God), and the gameplay is so perfect that other than the lack of scanlines I can't tell the difference between it and the arcade PCB when I'm playing it. It certainly looks 10x better than playing it on an LCD. I should add ver 1.1 and X360 mode look stellar on an RGB monitor. Really beautiful actually.