I treat it like any other "sand" substrate. Hover over the top to pick up some of the noticeable mulm near the front, but otherwise leave some around as fertilizer. I certainly would not dig down to the organic layer.Once you get stocked are you planning to do gravel vacs when you do water changes? With all those plants and the wood, plus that fragile substrate I'm thinking vacuuming the substrate could be dangerous and more hassle than it's worth.
Yes indeed, the ladies like your wood! How's the cycle coming now? It can't be long...Looks good, man. I bet the ladies just love your big wood.
I haven't tested lately, and pH limitation could be the case, but with a 7.6 pH out of the tap it would have to drop considerably to be limiting nitryfying bacteria to such an extent. Granted, it's only been a month. The AOB seem to be doing fine, just the NOB step is not up to par.It looks great!
I think I know waths happens. Test the ph value...that big wood may be is the source a low ph in your tank = slow cycling (2-3 month). Nitrosomonas and nitrobacter need ph 6,8 or more to multiplicate fast. Try to add an air pompe to increase the ph (ideal value 7,5-7,7 during the cycling). Plants used in the time of cycling is considered "of sacrifice"...It's just my opinion...Good luck!