As usual, not explaining everything.
cooperation with local churches has rendered RPC-514 isolated to the island of Manhattan.
I think it may be best if the exact location of the churches are pointed out. It took me too long to figure out where local was.
Local religious authorities have agreed to continue efforts to definitively isolate RPC-514 to a smaller area, however this process is currently unsuccessful.
It just feels a bit strange, you know? Maybe it's just me. How about "Efforts to definitively isolate RPC-514 to a smaller area have been agreed to by religious authorities within Manhattan." The "unsuccessful" part can be left to the description, no?
Authority personnel are to be equipped with armaments specifically outfitted with religious symbolism , in order to abuse RPC-514's sensitivity towards said symbolism.
Strange spot for a comma. Maybe remove the comma?
and bare physical resemblance towards biblical demons.
I think it's "bear".
as the shareholders in these buildings refuse to allow Authority agents to remove RPC-514.
I think "have refused" would work a bit better.
Although RPC-514 instances nest like their non-anomalous counterparts,
Sentence could use some restructuring. How about "Although RPC-514 instances conduct in nesting,"?
It is unknown at this time how RPC-514 do such things that would be required to add to a building such as rewiring rooftop electronics, connecting air ventilation systems, and/or rerouting of water pipes.
Doesn't sound clinical enough, I suppose. Try "undertakes actions", see if it works.
When this process is fully completed, the building will appear non-anomalous from the exterior, however have a noticeable lack of any interior infrastructure in the areas that were added by RPC-514 instances.
Again, another misuse of "however". I think changing it to "but will" could help.
All in all, I have 2 things that I think you could do with the writing. First it to use a bit more passive voice, second is to use "however" properly. Good job nonetheless!