well.... I just read pretty much the whole thing the last couple of days, I have a comment to maybe help.... If I remember correctly you said the rubber liner guy told you that you could spray it on with a gun. Would that not allow for a better application ? Perhaps you could get a spray gun, borrow a air compressor if you don't have one... take the other guys left over rubber liner that he offered to ship to you.... take a couple days and just spray the crap out of it... at least 10 coats or so... I think this should really help do the job....
I agree with the concept that you were only putting on small bandade over the "wound" per say... and then when you filled it in started back again.... with a nice and fluid application of 10 or so more layers.... you should have enought coverage over the "wounds" lol to seal it for good.
I have really enjoyed your build, and wish it all the best. Since you haven't ordered the pond liner yet and won't for a few weeks as you pointed out.... plus you believe in your rubber product and said it was your application method, change your method, spray it on. and lets get some water in there....
also... maybe you can get some more of the tape you once used on the bottom and line the tank with it around all areas that maybe be leaking in your opinion... if there is another material you can use instead that is cheaper... that would work as well.... it would be great if you could just cover the entire thing and use that as "ground zero" and everything under it as just extra...