nintyalex's findings

The Koopalings all use the same bank and id. The first digit on the second-to last byte shows which Koopaling is fought (they use the corresponding world number from the main game; thus, Ludwig is 7, Larry in Airship's Revenge is 1, and Lemmy in Armored Airship is 6). The second digit says how many stomps they take to beat (3 by default, up to 16; 0 is automatic death). The last byte tells how many fireballs are needed to beat them (10 by default). The graphics are garbled if they are set to any other Koopaling (and Wendy's rings are invisible!), though.

Similar rules apply to SMB1 Bowser. The second-to-last byte shows which enemy is disguised as Bowser (11 gives the real deal), and the last byte determines whether he breathes fire or throws hammers (even for fire, odd for hammers). I haven't gotten him to do both, though...

I bet the directional lifts and giant blocks you found are just the sprites used when they are hit; the actual objects must be elsewhere.

The main game levels on the rom are built just like the (S)NES versions of the game, just with the new byte organization system (I figured this out while trying to reverse the level design changes.).