Skipping the transformation sequence you talked about saves hell of a lot of time, and most people doesn´t know about this little trick.
Also, death warp is also a good way to save time, but in a 100% run, you should only take enough damage during the boss battle if you´re gonna use death as shortcut later on.
Since several items lies deep inside some areas, you might be forced to take damage during the walk, so be sure to have enough health so you dont have to avoid enemies.
When all items are picked up, use the death warp.
For fastest time, try to have 0 health every time before letting an enemy kill you.
You said in your run that you didn´t pick up any of the attack items?
You know that you will save time during the boss battles if you have a more powerful attack with your regular weapon since the special weapons only let´s you do damage to a boss every 8 frame?
It is faster this way i think!
The trick you use on the Optomon works great if you are doing a low % run (any%), i´m not sure if it´s necessary in a 100% run, you have more powerups then and your attack is a bit more powerful.
And each time you press the select button to choose one of the weapons, you lose frames, correct me if im right...55 or 56 frames from that you press select to the game let´s you continue.
I have done a any%, but i cant submit it here for some reason, i´m afraid the fm2 file have been damaged in some way.
I´m going to continue on trying to get it up here, but if it doesn´t work, i´ll have to do it all over again.....this game needs to be up here.
Tell me when you or anyone else are about to start working on this, i think i can help out too.
Let me know if you need some tips, i´m experienced when it comes to this game, it´s one of my favorite nes games.