Wow lots of good ideas amd observations.
I think the basic thing in your situation is,"do what you can".
Filtration, if possible, is most important, many of those nasties love to live on the particles and removing the particles will remove many of them. Is it now save? No but safer...
If you go with taking acid directly from the pressurised acid supply, I would suggest using a mixing tee lined with teflon or other protective substance. I would also strongly suggest a very good non-return valve on the acid line. I have seen a pressurised acid line spring a leak, twice in a...
What What are the climatic conditions in your area? If the area where the hypo is to be stored is subject to high temperatures you may need to take that into consideration as high temperatures increase the rate that the hypo loses strength. You may need to limit the amount of storage and depend...