Wow, thank you for the response all!
A lot of information here so I am going to randomly answer questions and address advice then simply tag you all...excuse the laziness.
Extremely interesting that barely anyone else has had issues with excel and their cories, which leaves me looking for alternative issues. NH3, whilst it appears to be at .25ppm in tests, I refuse to believe this. Though the tests are the only thing I have to go on, I cannot in my right mind accept that I have shrimp and fish acting perfectly happy without issue living in any level of ammonia. However, I will test again, water changes today as well.
I will try peroxide treatments as well...this has recently also been ineffective on the algaes I have had. Perhaps this is due to misuse, but it had been 100% successful prior to this tank and now nothing seems to be damaging this algae. Let's see how it goes.
I have a feeling that there is a huge imbalance in this tank fert wise. I am wanting to figure it out, but probably need some assistance on where to start on a new batch of ferts for low tech...things could get much worse before they improve. As far as removing rocks etc, cannot be done...not without ruining the entire scape sadly.
I actually think some signs from plants are showing deficiencies, red/yellowing at the top of cabomba (if that is what this plant is) plus increased inter-nodal lengths.
BBA in this tank is most likely cause by organics of course...but cleanings are incredibly difficult to accomplish in this set up and I am not sure why there would be such high levels of organics.
At the end of the day, I am a tad confused by this tank in particular. Since it being set up nothing has truly 'settled' and it is getting me a bit frustrated if I am honest. I would love there to be some easy fix, but I feel these are the outcomes of a tank in perpetual fluctuation with no easily foreseeable change to that.
For my habrosus, I will note any changes in behavior and colouration after maintenance etc. I will try everything I can to keep both fish and plants happy, but fish first in my eyes.