I think it's still pretty confusing, but it should be much better now.
And there are a couple sidequests and a hidden boss, so there's that.

There are three floors to the garage, and there is a maintenance door on the top floor that leads to the roof. You should walk to the ladder as soon as you go through the door. You just jump to climb up, and hold crouch to climb down. (In this case, climbing down might cause you to fall into the parking lot, so probably shouldn't do that).

This thread getting posts made me to try to play the JFIMA again, and I ran into two pretty annoying bugs close to the end of the game. One of them isn't that important (I can't explain it without spoilers, but I eventually found a way to fix it in-game).
The other caused the game to crash when I beat the final boss, which definitely should not be happening! Judging by the message I got, this is probably because I was playing from a save file, and a null pointer happened because maps from before that point hadn't been properly loaded. Since the map constantly expands as you advance in the game, there's a good chance that if the game crashes, it will be because a map got mixed up somewhere. I'll try to patch it quickly (I'm sure there are some other bugfixes I never got around to uploading, so this gives me an excuse to deal with those as well).

which ramp is it? up or down?

The up ramp. The down ramp leads to the basement.

Saving doesn't save your exact position, just what events you've completed, your stats, and your items. So loading will start you at the respawn point for whichever section you're on.

I've found lots of things to improve with the extra ending sequence, but that really doesn't warrant an update on its own. I guess there is a bug with loading that I should fix (though I doubt anyone who discovers it would do much complaining. ).

Most of the boss fights require something special to complete, and some of those probably aren't as obvious as they should be (Particularly the first one...)

I'm not falling asleep like I meant to and my room is haunted by mosquitoes, so I might try to get virtual audio cable running and see if I can do anything useful with it.
That, or record some kinda playthrough, but words would be more helpful, I'm sure.

You don't need to switch controls to switch characters; hold the inventory/party button, press left or right, and then crouch, and you should switch characters.

As for that boss...

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The trick is for the seaweed to hit the tower while it has him stunned. Which unfortunately turned out harder than I hoped it would.

The seaweed will only hit the tower at the end of the attack, so you need to be a few steps away from it. Which means that Wave needs to be between you and the tower when you hit him with it.
Wave doesn't like to make that easy, so I usually stun him with seaweed first, and use the opportunity to get into position.
He does have to be weakened a bit first, but not by much. If you have both characters there, but the AI isn't helping, it probably means he's weak enough.

I think the tower is around (7, 5), and the hit area of the seaweed is about three tiles wide, so I'd just try to get close to the edge of the map on either the column or row and try from there. (I usually do it from the south (like y =9 or so) or west (x=1 or so).

Did you try going inside the student union (by where you got the seaweed)? You can talk to someone in there if you follow the noise.

Dying doesn't undo your progress; even losing everyone and respawning just puts you back at the current spawn point.
Hm, I never thought about beacons for locations, actually... not a bad idea!