Stool transplantation (technically fecal microbiota transplant or FMT) via endoscope has become the "standard of care" for recurrent C. diff infections with a ~90% cure rate. FMT has also shown good efficacy for pouchitis with or without the presence of the C. diff pathogen.
https://www.health.harvard.edu...ctions-2019050916576
https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4834257/
https://www.researchgate.net/p...on_FMT_a_case_report
A clinical using FMT for chronic pouchitis trail was completed at UCSF April of last year but the results have not yet been published. You may check here from time to time for the results to appear:
https://clinicaltrials.gov/ct2/show/NCT02428361
In your shoes, I certainly give FMT a shot before reverting to permanent ileostomy.
Best wishes or you