To treat SIBO plus Candida I would add the following to the SIBO protocol.
1) Start taking a polyene and a triazole antifungal before the Antibiotics , and continue them right through the SIBO process and afterwards. Ideally, identify a polyene and triazole that works for your strain of Candida. For example I get lots of die-off from oral amphotericin B, but nothing with nystatin. Fluconazole also does little to kill my Candida.
2) Do an enema HPI after finishing the GSE. This should replace the good bacteria killed by the Antibiotics .