The pH of your saliva is very unreliable - it may or may not mean something. Urine pH isn't perfect either, it's time-delayed (I think of urine pH as the "bodily average of the last 3 hours").
"My doctor put me on enzymes, HCL and anti-fungals and it is has been over a year. Is it possible that I have been doing this stuff for too long and I'm now on the leaky gut side of things?"
Leaky gut is a by-product of hyphal/fungal candida. So if you didn't have it before but have it now, it would be b/c your candida has gotten much worse. But the 3 things you mention are not going to "erode" your gut and thereby lead to "leaky gut," that's not how it works.