If you can, check over SSH what htop/the logs say. If you can't, just check the logs (search for ;dm from the Homescreen), there may be some more tricky cataloging/indexing stuff involved.
As for the custom stuff, AFAIK, the ACX should be inert, and for the fonts, unless you're using a seriously broken font (or one that the framework subtly doesn't like), the impact should be minimal.
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