When I setup the 3rd node as a secondary DNS, will it matter if Server 1 is mydns and Server 3 will be bind?
This does not matter.
(I'm going to attempt a mydns -> bind switch at some point but I need to gather all the threads first and determine the best method)
1) Stop ynad uninstall mydns
2) Install bind and switch dns server to bind in ispconfig under System > server config
3) run the ispconfig update with reconfigure services
4) login to ispconfig and run the resync (Tools > resync) for the dns records.
5) Check the file /var/log/syslog for errors. Mydns is more fault tolerant then bind in some cases, so it might be that bind complains about syntax issues in some zones. Check the zones in ispconfig dns module and correct the issues.