Too late for a medium transfer?

Hey guys ive been doing a "bubbleponics" setup for the last couple weeks (18days to be exact) using a rockwool cube surrounded by lavarocks in a jerry rigged netpot. The entire time i have been experiencing wild PH fluctuations. I thought this might be cause of alge, so i light proofed the res (again)... then i thought my meter might be wrong.. nope... so the only option left i can think of is the lavarocks right? is it too late to try to transfer into perlite? The pots i am using would require me to have some lavarock at the bottom to make sure the perlite dosent fall out but i belive it would vastly help my situation!
Comments/suggestions/telling me how stupid i am for using lavarocks is welcome
+rep for info! thanks!
link to full journal from day 1 is in my sig