I'm delighted to see you call yourself 'Enthusiastic Processor', at least your difficulties have not gotton you down.
You will find a huge difference with the external too.I never looked back. It will take some time to build up bacteria etc. I wouldn't even bother thinking about cleaning it for a number of weeks at least.
At the moment just keep checking the water for ammonia and nitrite until you get these down to 0. (Continue to monitor the ammonia - just in case ) Your water changes will help stop these from getting too high. Remember, mix the stress coat with the water in the bin, prior to putting into the tank.
All going well soon you can drop down to a weekly water change of 20-25%. In fact the water changes in a cycled tank are to control the nitrate levels - although they do give us the opportunity to clean the substrate of any nasty 'crap' that has built up
Please let us know how you get on over the coming week or 2
Monty