I agree a run of this will take more planning.
I've checked gamefaqs, the walkthrough there could be more helpful but it seems to give the shortest route in most situations, assuming 100% collection of weapons and spells is desired. Which I'm not sure it is, but I think getting all or most of the spells is worth it because learning magic also increases MP, and some very useful spells (such as Unlock) consume lots of MP which takes time to get refills for. 100% weapons is probably not the fastest way though, but the dagger (1st weapon) is required and the shuriken (2nd weapon) seems to beat enemies a lot faster than the dagger.
Which weapons and spells are optimal to use is the main thing I'm not sure about, and it's the real main reason I'm currently not continuing to do the run past the point where the optimal choices are obvious.
I hadn't checked david wonn's page, but now I have and it has no particularly useful information on this game. Well, actually, the save and reload trick to warp to a room's entrance could save time, if that can record properly. About skipping dungeon 3... it would have to be done later on anyway so I don't see how doing it out of order would be faster.
The game has absolutely no element of luck to it, as far as I can tell, so it's too bad that can't be manipulated. (Actually, maybe the timing of appearances of the overworld enemies are random, but they don't matter anyway.)
The world map can be rotated to reduce the time it takes to walk around there. (shorter-than-manhattan distance if done properly)
The collision detection is extremely strict, compared to what the size of the graphics suggest, although jumping at just the right moment can give 1 extra frame of leeway for squeezing past enemies.
The character can only walk in 4 directions, although frame-by-frame alternation can sometimes make it look like 8 directions are possible, but it's not actually any faster for moving diagonally. Jumping and walking are exactly the same speed, but falling instead of jumping from a block is very slightly slower. It's possible to walk on the very edge of platforms around enemies that are on those platforms. When casting a spell, there is a movement delay which can be skipped by jumping.
Weapons can be fired a lot faster than probably intended (i.e. autofire basically works) and with multishot weapons can be fired in multiple directions at what appears to be the same time (really 2 frames apart). It's also possible to shoot in one direction while walking in another direction, and to alter the speed of the projectile somewhat.
Being closer to enemies saves a lot of time since the weapon hits sooner and all the game cares about when deciding if you can fire another weapon is how many of them are currently in the air. But if too close to the enemy, for some reason the weapon always "misses", I'm not sure if this is a bug or feature but it sure doesn't help.
The only possibly useful bug I've found is that fired weapons that are still in the air when changing weapons will transform into the new weapon in midair, even if it shouldn't be possible to have that many of that kind in the air at once. But I'm not sure if this change is more than graphical and it probably wouldn't save any time anyway.