I gave up in the end, achieved my goal by
- Uninstall msmq with http
- Stop Default and 'target' website (I actually didn't do this but should have!)
- Go into advanced settings in IIS and change the Site Id of Default website to '99'
- Go into advanced setting in IIS and change the Site Id of 'target' website to '1'
- Restart IIS/Server up to you.
- Check that websites still work!
- Add MSMQ with http feature back.
Done, I have MSMQ installed where I wanted.
NOTE: I had to manually add the bindings for net.msmq and msmsq.formatname to the 'target' website. The installer didn't do that this time (nor did the uninstall remove them from 'default website').