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Try adding the game in Steam and enabling Steam input for it. I was able to play both Theia Crimson Eclipse (RM2K3) and the PC Zelda 2 remake (Game Maker) with my DualShock 4.

I don't know if cakes restore skills... Just TP. 

But yeah, I won anyways. 

The healing worked properly in the final dungeon. 

Whew. I beat it :) The last dungeon was pretty creative, and the ending is satisfying but promises more adventure. Where are you Sega?!?! 

Also, please read this fan fiction: it's not mine, but it's my favourite Phantasy Star fan work ever :) 

http://www.phantasy-star.net/fanfics/mathews/child.html

Same thing in Torinco: a character rejoined my party with their HP and TP restored, but I had to rest at the Inn to restore their skills. 

Thanks for the game :) If Sega is Lutz, then you are Rune. 

Unfortunately, I found a minor bug: there were two instances in which my party was healed but my skills were not restored. I had a plot party heal, and I took a free rest at the tent in Zema. Not having my skills restored made the underwater power plant boss more difficult, but I still barely managed.

I suspect that your skills do not restore unless you rest at an Inn.

Also, I just beat the Blind Sandworm, but I have no idea who in Tonoe will make me my special armor :(

So far I've been lucky. I just beat the boss of the Tonoe Mines (no spoilers lol) and had no issues with the font or with my Dual Shock 4.

The game is pretty straightforward for me, and I've had no trouble progressing the story. Perhaps because I'm playing it right after a Phantasy Star 4 replay. 

I hope your game is complete so that I'm not disappointed at the end, but I'm very happy so far.