New email in the early hours from Magento states that they will be producing new patch versions to deal with the SUPEE-1533 and SUPEE-3941 compatibility issues. So maybe just hold your horses for a bit.
ENTERPRISE EDITION 1.14.3, COMMUNITY EDITION 1.9.3, AND SUPEE-8788 Enterprise Edition 1.14.3 and Community Edition 1.9.3 deliver over 120 quality improvements, as well as support for PHP 5.6. They also resolve critical security issues, including: ...
...The SUPEE-8788 patch addresses these security issues in earlier Magento versions. Unfortunately, we have discovered that the SUPEE-8788 patches for Community Edition 1.8 and earlier releases and Enterprise Edition 1.13 and earlier releases fail if a store has previously applied SUPEE-1533 or SUPEE-3941 security patches. We are working to correct this issue and will provide new patches in the next one to three days. Until then, we are removing these versions of the SUPEE-8788 patch from distribution...
However I am concerned that my active Magento versions fall between the CE 1.9.3 that they say works and the new versions coming soon for V1.8 and below. I have contacted them so will wait and see what they say.