I feel hesitant myself to use glass anything in DIY CO2. Those plastic bottles are meant to withstand a good deal of pressure. However, as what I mentioned earlier, a gas separator/bubble counter that's too large would take A LOT of time to fill up with co2 to displace o2 for there to be enough working pressure. For this reason, you can use a small gatorade bottle for a DIY bubble counter OR do as what I did and use a
Fluval bubble counter, which IMO, works great and is small and not expensive. You'll at least be able to eliminate that part of the DIY system as a potential source of a leak. I wouldn't remove a check valve, unless you want to come home one day and find that your tank water has siphoned out. I use a check valve between the bubble counter and the diffuser without problems. You just have to make sure that you placed the check valve on the line oriented correctly, as co2 will only pass in one direction in the CV. My CV has a little arrow showing the direction in which gas will flow through.
Anyway... here's my DIY setup.. works like a charm on my 12g and it's been going strong for about a year.