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Sorry for late reply, but for what's it's worth, here is my response

Thanks! And, in hindsight, I agree that I may have gone overboard in some places, specially endgame. I guess my reasoning/thought process when I made this was that I wanted a challenge even with a maxed out party. That's why the final dungeon is as brutal as it is. Personally I really enjoy having a maxed out party and still have trouble with random encounters.
Using Proud Clod isn't too hard.
Open scene.bin (obviously).
Under the top manue (file, Search, Dump Data, etc., etc.) there is a dropdown where you can select what scene to edit. A scene is basically a collection of enemy data, battle formation and AI. You can search for enemies by names. Keep in mind that most enemies are in multiple scenes. One enemy can have different stats for each scene they are in.
But in your case you just want to edit bosses. Omega is in scene 5. Select scene 5 in the dropdown. After that, click "Enemy Management" in the top menu. Here you can edit stats. When done, save. You may be prompted to update kernel.bin (iirc), if so, select yes/ok.
Ma Bino Gi On Modron may use an animation id that could crash the game. You want to go to scene 254 and select the modron attack in the list on the left. Chenge the attack Animation ID to another hex value. A safe value may be AE (same as) Mabonagrain.