I have been using the homemade baubble cloner for quite some time now,and have experimented with it plenty. I have used Ph 5 all the way to 7.6. Hard water, and R/O. Stems in the water,and out. Dome , no dome.
From my experience water PH does not seem to make a real huge difference. Strain difference seems to be the biggest single difference. For instance AK47 roots much faster than Blueberry. A dome is not necessary, a little spritz the first day or too, should do the trick. They will quite likely look wilted after their first 6 hours or so in the bubbler. Check back in 24, they should look great. Also you do not need any cloning gel, or any other rooting agent. Just be patient.