It depends on what you want out of all the possible rewards from this thunder raid event. Ultimately, if you don't want MLB versions of Yggdrasil and the thunder weapon (note it's skill of +HP), e.g. you don't play thunder element team, then one copy of each is enough for collection purposes.

Still, I have a question about your AP usage. Generally, it makes more sense to just participate in others' raid calls using your BP points and refill as needed with energy seeds. I think Sanahtlig once calculated that if you MVP consistently in the event raids, your energy seeds expenditure breaks even from the event gacha loot and the PP/soul milestone rewards. At least I do. I started the day at about 210 seeds. Now I'm at 1 million PP and around 200 seeds. So unless you try to spawn Ragnarok raid, I would say use BP instead of AP as your main source.