Anytime you start stacking gain pedals on top of each other there is a high potential for unwanted noise. Even though each pedal is set fairly low when you layers them it adds up. Have you tried all the pedals in the signal without stacking the gain pedals and just used one gain pedal by itself to see what the noise level is? I would have all the pedals I use in the chain and just use one at a time and see what produces the most noise. I would add things in from there (meaning turning on more than one pedal at a time) and see what it is that is pushing things over the edge. That would be a good way to isolate things.
On a side note, I don't know that it is completely necessary to use a bunch of gain or drive pedals together on low settings to achieve your desired tone. I don't know your rig and I don't know what your desired sound is so maybe it is necessary but I lean towards it not being the case. The more you add to the chain, the more chance for issues of all kinds.
Regarding JHS pedals being noisy, the few have are not noisy and work well with other pedals. If you do feel you need to use multiple pedals stacked to get your tone, I would throw some noise gates into the mix as well.