"You should closely examine the caps and the alignment on the head that is mostly plugged."
Do you mean that its not sealing, so its not soaking?
It will soak fine, cleaning solution from the lint free makes contact with the bottom of the head.
Immediately after you soak you should do a strong clean.
If the seal is not sealing properly, it will not have enough vacuum to remove any plugs from plugged nozzles.
http://www.mutoh.com/kb/entry/95/
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