It's been quite awhile for me since I finished Xenogears, so I don't really have any specific strategies remembered, but try this:
Just destroy all those orb things that are floating around, which will then strip down the final boss' techniques and features, thus making the boss not very difficult to beat. But as you may have already experienced, fighting the various attributes of the boss is a bit tough and tricky, so sacrifice your weaker characters in these battles (hell, even use Chu-Chu) and keep your best 3 guys in tip-top shape for the last battle.
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