When the lease expires, if you want to keep her, I would amend it.

I would then make a note of this and amend your lease for next time so it is spelled out in the lease. 

Chalk everything up to experience, amend your lease, go back and do it again next year.

If permits were not pulled/ there is not an amended certificate of occupancy, the systematic code enforcement inspectors will almost certainly order the units converted back OR require permits to be pulled and proof that the conversion was done to code (assuming that is even possible).Additionally, under rent control, you will then need to credit the existing tenant for the loss of the amenity that occurred when they lost a bedroom.Proceed with extreme caution as SCEP inspectors do not mess around . . . 

I also am wondering what I need to do to amend the rental agreement to include him.SF bay area/$1,300 mo. ~ water and garbage paid by me.Thanks in advance.

We also have tenants sign off on this form:DISCLOSURE OF INFORMATION ON MOLD AND MOISTURE HAZARDS(Addendum to Rental Agreement)The Rental Agreement dated _________ between ____________________________ (Landlord) and _____________________________________________ (Tenant), of real property located at __________________________________________________, is hereby amended in include the following terms and conditions: “Disclosure of Information on Mold and Moisture Hazards.”

If not, then amend the rental agreement/lease for the addition of another occupant.

But this is surpassingly irrelevant as I have no duty to anyone but myself to enforce the terms of my lease and I am free to amend those terms to make them more permissive at any moment.Under these facts I don't think the case is susceptible of a neat solution.

If the lease doesn't provide for it, you can't legally charge them a late fee.You can, of course, have this woman sign a new lease (or amendments) at any time, but she is not required to.I agree with most here that she is not a good tenant if she is paying late.  

or should I amend with a tenant removal and add the new co-signer/co-tenant onto the lease?