Okay, lets head back to basics and review everything. The symptoms you've described clearly indicate an air intrusion. Air can enter the system without allowing fuel to leak. You've got to start at the beginning of the fuel system and examine everything, all fuel lines for cracks, all connections, everything. You're sucking air somewhere. Consider replacing all screw type hose clamps if you have any. They sometimes allow air to enter. The high pressure fuel injections clamps are superior.
You stated several times that you've used fuel rated teflon. If a connection has an "o" ring or an olive, then that "o" ring or olive is the seal, and there is no need for teflon tape. If a piece of the teflon break loose and gets to the IP you may have a significant problem.
I think you said that you replaced the injectors, all 8 of them I hope. Did you remove and replace the copper washer in each injector bore? A copper washer must be present and properly seated. Two copper washers, failure to dig out an old washer, will cause problems. An injector without a copper washer, or an injector with 2 washers, may cause an air leak directly into the cylinder. I don't believe that would show as bubbles in the clear lines you've installed.
Lets review also what you have installed, either new or not. List everything you've replaced, including name brand and purchase location. There are a very limited number of parts dealers who have earned our trust. It's way too easy to walk into a parts store and buy a POS part, thinking you've gotten a good deal.