I have also had this problem with Notes 9.0.1 Fix Pack 4 with sending outbound SMTP directly from the Notes client and getting "Replicator Error SSL bad peer certificate. Connection refused". Today I tried again to install Fix Pack 4 and the latest hot fix (901FP4SHF292_W32_standard.exe), and had the same problem.
The only work-around that I have found is to re-run the Hot Fix and/or Fix Pack 4 installers to revert back to Notes 9.0.1, and then install Notes 9.0.1 Fix Pack 3.
(Unfortunately, Fix Pack 3 has other problems - like problems importing OSGi plugins into an update site.)