The earlier requires prior authorization from the tenant (either in a lease clause or written amendment) to apply security deposit to charges. 

How much will they be to create, amend, and review each year?

You are still held liable if they commit a crime on your property. 2012    Continuing issues with substandard housing conditions Rental Registration & Inspection Ordinance SMC 22.214 revised program developed with input from local rental owners. 2016 Significant rate of discrimination based on use of Section 8 voucher, disability and familial status found during 2015 testing program Source of Income Ordinance and “First in Time” rule SMC 14.08.020 amended to include source of income as protected class.

I would just do a contract amendment to remove her as long as the other roommates agree and require one payment be made for rent.

After doing so, review and amend (or have your attorney review and amend) those contracts so that it's acceptable to you. 

On line 14 where it states "Application of Rental Income"...it says section 1402(a) is amended by striking paragraph 1.

Is he making amends and accepting responsibility for his error in judgement?

In Denver for example the Montbello sub-market which is typified by low clear, poorly loaded undesirable properties experienced a resurgence after amendment 64 was past.

Here are my questions.Can I amend the payment clause in the contract and require that tenants pay rent using an online service?

—Subsection (a) of section 121 is amended—(1) by striking “5-year period” and inserting “8-year period”, and(2) by striking “2 years” and inserting “5 years”.