Ok, test run is completed. Got it under 43 minutes, beating the old WW run and beating the published run by over 9 minutes.
http://dehacked.2y.net/microstorage.php/info/563862445/Crystalis-test1.fm2
http://dehacked.2y.net/microstorage.php/info/1136653041/Crystalis-test2.fm2
My new special grinding technique is in the Styx cave on Mt Hydra. Otherwise I use the same locations to grind but do it much more efficiently. Look for the new glitch after grinding on the spiders in the fortress. Another point of interest are both fights with Mado. In a strange glitch, I'm able to skip some dialog after getting the thunder sword but end up having to see it later when I fight Mado in that room.
I kept finding speedups through the end. The big dragon boss fight is 15 seconds faster by using a special technique to manipulate his laser attack. The tower area at the end seems pretty straightforward, but even there I found enough changes to speed it up by 15 sec.
In the second half I did a lot more work on managing experience. This saves a ton of time and cuts down on grinding. In fact, a large portion of the time saved is cut directly from time spent grinding.
Needed two files due to file size. But I can cut file size in half by disabling controller 2. For some reason it didn't work when I tried to hack this with a text editor. I'll remember this for the final run. You can combine these two files into one in a text editor. Go to frame 86511 in the first one and delete everything after that. Then paste the input from the second one.
Make sure you have "old PPU" set, otherwise it will desync.