No problem, I probably should have implemented a check and added a notification to LALE to help people avoid this issue.

I believe that you are using a Link's Awakening ROM that isn't version 1.2. When I created LALE, I specifically worked with and programmed around a 1.2 Link's Awakening ROM (Legend of Zelda, The - Link's Awakening DX (U) (V1.2) [C][!]). Using other versions results in unintended exception problems.
You can check your ROMs version by using a hex editor and looking at the value at 0x014C (the value should obviously be 02).

I've updated the topic to contain a .zip file that has an IPS patch in it.

Based on what you've told me I am unable to discern what the error may be. There certainly shouldn't have been any error created by you editing the warp and I am certain there wasn't as I tried myself and you said that its happening throughout the ROM now.

My only guess would be that you somehow wrote text over some important data in the ROM and it is now causing issues all over the place.

If you are seeing a portion of text you've written and nothing else then it is probably exactly what you said (the text was longer than the original length). There are no set lengths for text in Link's Awakening, the game just has pointers as to where to start reading text from and then a marker so it knows where to stop. For the Lanmola text the game is still reading from its original location which is the owl statue text now.

To fix this you will have to use the repoint tool that is a part of the text editor. Basically you find a new address (for this you could just go to whatever location is after your owl statue text, which would probably be the remnants of the Lanmola's text) and then you will repoint the Lanmola's text to that location. Then you can just edit the text at that location and the game will read it from there. Alternatively you can open the ROM in a hex editor and look for free space (00s) and repoint to a location that has adequate space for the text you want.

I don't really remember much of what I did for the lame bosses I made. It was a combination of spawning them, altering properties, setting room flags and crap in ZOSE. Sorry that I'm not very helpful, but it has been so long.

Within the text editor there is the text re-pointer (blue arrow at the top). This allows you to change what memory location that game will go to for text. Simply click the blue arrow and then find the pointer of the text you have overwritten. You will have to find a new location in the ROM to point to. There is a lot of free space that can be found using a hex editor (00s), as well as other languages using up space that you could simply overwrite. I do believe you can point to anywhere in the ROM.

Please note this does not transfer the text at that location over to the new location, it simply tells the game where to get the text from. You will have to do that manually.

The memory address CC99 is the YX  coordinates that Link is currently at so by performing a checkmemory CC99 35 the script should wait until Link is at that location.
As for the second question I do not know of a memory address that will subtract some amount X from the rupee total. The addresses C6AD and C6AE are the total rupees the player has so you could change it to a set amount, but that isn't very useful.

I have not a clue. I tested it myself and it appears that only the maps that contain warps originally can be edited to warp to new maps, but I could have sworn that wasn't the case.

Currently I have no answer as to why that is. It is definitely something related to the game itself and not the editor though. That is really all I can say for this issue currently.

In fact a lot of things are hardcoded into the color dungeon.  This game actually contains tons of room specific data that's hardcoded into the game.

The unfortunate truth about LA. There are so many small exceptions with many of the editors because there will constantly be hardcoded checks for a things. If you are actually debugging and hex editing to make a superb hack it isn't the worst thing (certainly not that great by any means), but for making a level editor it is the biggest pain.

I thought I mentioned in the video that the Sprite Viewer/Bank editor didn't work with the colour dungeon, but if I didn't then whoops. I know I didn't mention it in the readme file when I probably should have, but once again whoops. Basically you can't edit the colour dungeon's sprite banks yet so that isn't really a bug, I just forgot to disable it and give any mention of it anywhere.

Yes this is apparently the case for any dungeon below B (except A working as an indoor map defaulting to map 0xB6). Perhaps there is a dungeon minimap beginning byte I missed and could add to the editor or something, but I will look into it sometime and I will probably post if I've got it working.

Yeah I suppose. The two are equivalent, I just used the term region for dungeons above 8/9 because I thought it would make more sense than say dungeon 0xAF or something.

So it does. Thanks for reporting the bug, it will be taken care of.