The music changes are definitely a step in the right direction, but there's still some improvement to be made.
Here's a few tips for you.
Firstly, you can use 'Stereo track to Mono' from the Tracks menu to convert the song to a single track. It sounds almost the same but reduces the filesize, and makes it easier to work with.
Secondly, metadata tags. You don't have to have the loop start at the beginning of the track and end at the end. By using metadata tags, you can avoid losing the intro to songs like Gritzy Desert.
To do this, you'll first want to click the arrow next to one of the selection viewer windows at the bottom so that you can view the selection position in samples as opposed to minutes and seconds. The metadata tag uses samples, so you'll need these numbers.
Next, find a point in the song that makes for a good starting point for your loop. It can be a part that's easy for your ear to recognize, or a part where the waveform stands out somehow. Once you've selected that point, make note of what sample number it's at. I like to have a .txt file open to record these numbers. To really make your loop sound pristine and hard to detect, pick a point of zero amplitude on the waveform.
Do the same thing with finding the endpoint to the loop and again, make note of which sample number that's at. You can use Ctrl+1 to zoom in and Ctrl+3 to zoom out, so you can pick points precisely.
To test your loop, highlight the whole section of the loop, hold Shift, then click play. This will play the selection and loop it when it reaches the end; ideally, you won't even be able to hear when the loop happens.
Once you've got the whole loop section picked out, note the length of the loop in samples. The endpoint doesn't actually matter; what you need is the start point and the length.
If you want, you can trim off any section beyond the loop to cut down the filesize. (You should also trim the start so there isn't dead space before the start of the song.) Another good idea is to amplify the whole track to match the amplitude of the other songs you're using so that the volume is streamlined. It's nice when you don't have one song that's way too loud or way too quiet.
Once that's all done and you have the start point and loop length, you're ready to export. Use Export Audio (from the File menu) and you'll get the option to add metadata tags. Add two tags and call them LOOPSTART and LOOPLENGTH. For their values, enter the values that you recorded earlier. Export the file and it should work in game!
I've attached the Skull Dungeon theme after I reworked it by following these steps so you can see what it looks like when it's done. It seems like a lot at first, but with a bit of practice it becomes pretty easy. I may not be able to beat people's tough levels, but I can make sure they have high quality music!