IMHO it's better to reset device completely (rather than removing parts of default config) and go from there (blank config):
/system reset-configuration no-defaults=yes
Then just assign addresses to individual interfaces and because it's router, it will automatically route anything it can.
If you do reset device this way, you must be prepared to connect using MAC connection. The reason why it didn't work for you before could be settings in Tools->MAC Server. So check those and test MAC connection before resetting device.