Sounds like you used this recipe. I haven't used it yet, so I cannot comment on it.
Tom, Gerryd, and Biollante all mentioned disturbing the sediment with gravel vacuuming to remove the mulm and mix the substrate. Some people attest to MTS (burrowing snails) preventing anoxic conditions. Some use kuhli loaches or some other burrowing fish. There is one mention about substrate particle size in Tom's post.
No, I don’t think 3 cm is too much, 3 cm is fine I tend to like 5 cm or so.
I have been using a lighter variation of the worm casting substrate for a few years now. Tom Barr’s mixture is richer and denser. I have just started the richer mixture myself a month or two ago.
I like Sphagnum Peat Moss (100% no additives), I like a layer under everything else, maybe .5 to 1 cm. Additionally I like to mix in a minimum of 10% of the volume into the substrate. If you are going to have heavy root plants I would mix up to 30% peat.
I rinse the peat; I like to leave the peat in bucket for a day or 10, strain the peat and dump into a pot (non-reactive) of boiling water, boil, stirring frequently for about twenty minutes. Strain the peat, let cool and you are ready. Peat moss tea, once cooled is actually good for your tank as well, in place of those ridiculously priced, so-called black-water extracts. The Peat moss tea is also good for your herb garden, potted plants and so forth.
I also like kuhli loaches, Pangio kuhlii, they are magnificent burrowers, in fact in a heavily planted tank with nice substrate you may rarely see them until you tear the tank down and find they have been breeding like crazy.
I didn't touch CO2, kept my usual trimming/WC/fert behavior. Even reduced KNO3 dosing by 33%
The filter wasn't cleaned: 4 months now running untouched
I deeply vacumed the gravel, like Tom suggested, over the last 4 weeks. Plants are doing much finer now, and I no longer see any issue with them. The parts in substrate of the P. Stellatus no longer rots and I no longer see spots of fermentation in gravel
No algae anywhere, except my lovely black spots on my root and filter outlets, but under self control (so unchanged)
Happy things are solved for now. The filter will be cleaned tonight though, with some of the water I kept after my WC of yesterday.