What is still not settled. Everything here is written as a question on purpose: none of it is guessed at in the listing.
Five stages have a target written into them at a fixed distance — 1, 2, 3, 4 and
scroll limit; and, in stages 2, 3, 4 and 7, that stopped screen is what sends you to the bonus stage. Stages 2, 3 and 6 have their own limit; the rest go through a counter at 0xE06C that only advances when the target is of a different kind from the last one, and at the third different one the limit becomes 0x01C0.
The route to the bonus stages is settled. What that counter changes on top of it is not.
Bank 3 ends with a hole of 399 bytes between the last data and the eleven bytes of the Konami mark. They are declared as a range, but what they were is unknown: they could be filler for the mark to sit at the very end, or the tail of something that was cut.
The table at 0x418F says which stage follows which once the ninth is past, and the listing reads it correctly. What is not measured is which of the twelve are reachable in a normal game and which only in the second loop.
One enemy in four comes out marked and one in sixteen comes out with a 2 instead of a 1. The 1 is understood: it paints the enemy red and changes what it leaves when it dies. What the 2 changes, beyond going through a different branch, has not been pinned down in play.
The stage 5 background engine dispatches on eight types of card, but the script that fills them only ever writes some of them. Whether the rest are unused or just rare has not been checked frame by frame.