We come from a religious background where treatment is based on faith and home cures. What can we use to treat end stage syphilis?

See a doctor. If you're saying that you have been treating syphilis with home cures, and it has progressed to the tertiary stage, that should tell you something: you could have resolved the problem at an early stage with a shot of penicillin. Since you didn't, you have a significant problem, since tertiary syphilis is quite difficult to treat. See a qualified physician immediately.
Forgive my frankness. It's too late now. Syphilis's dreadful effects could have been stopped with penicillin. If you are finally realizing that you have been deceived by an anti-medical cult, and somebody has end-stage heart or brain damage or is in chronic severe pain from spinal cord disaese, i would urge you to contact an attorney.
Not much. Antibiotic treatment is the only treatment that could make the situation better.
No . By definition, "alternative" is different than modern western medicine. Generally any drug, herb, treatment, or procedure that stands up to rigorous scientific scrutiny is included in modern medicine. The problem is that many alternative practices, herbs etc do not stand up to scientific scrutiny. May not work. may be deadly. They therefore remain "alternative". Be careful watch your $$$.