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I would recommend retaining a lawyer at this point. If you are working over 12 hours a day x 6-7 days/week, you don't have time to deal with this matter on your own.
You may have grounds to actually sue the city for their illegal entry into your home, and recover your attorney's fees via this civil suit.
The HOA has no right to tell you how to keep the inside of your unit. The HOA can dictate the exterior of your home (they may even be able to dictate how you maintain your vehicle - if it appears unduly messy and impairs the appearance of the association - this would need to be under an interpretation of your HOA's specific CC&Rs, but they cannot dictate how you maintain your interior).
You can find local attorneys using the State and local Bar Association directories, or private directories such as www.AVVO.com; www.FindLaw.com; or www.Martindale.com (I personally find www.AVVO.com to be the most user friendly). Look for an attorney that has experience with civil rights claims against public agencies (look for "42 USC 1983 experience" as a good way to find attorneys with the proper litigation background).
I agree with you, this is insane (and it is abusive).
To deal with the situation, it is probably best to break things down into parts (just as you would with a medical problem for one of your patients at work).
This would be dealt with in civil court.
No, this is not a criminal issue at all (my apologies, I thought you were asking about your claims against the police etc. - but no, you don't have any basis to worry about a criminal complaint against yourself for this matter).