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

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.  

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 . . . 

Amended by Acts 1985, 69th Leg., ch. 305, Sec. 2, eff.

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.

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

I found the agreement, in case anyone wants to see what I did regarding PayPal payments by roommates:Amendment to Lease or Rental Agreement This is an Amendment to the lease or rental agreement dated November 12, 2012, (the "Agreement") between Sue's Daughter ("Landlord") and Tenant A and Tenant B ("Tenants") regarding property located at 123 Madeup Street, Somewhere, CA ("the Premises").Landlord and Tenants agree to the following changes and/or additions to the Agreement: 1) Landlord agrees to allow Tenants, who are roommates, to pay their rent separately.

They claimed I violated their amendments ( they chose 2-3 of them), multiple acronym statute violations I've never heard of - (my lawyer even said they contradicted themselves too!) 

I think the reason why they are requiring the landlords to hire the inspectors is to get around the 4th Amendment problem of having a city government employee do the inspection.

Best to get a good lease from the start that you can always amend and improve.