My roof top system

[Tanktotable]

These tests are of the past two weeks. The thing is this system is on my roof. and its not covered. So when it rains that water gets into my system. I have found that naturally the system goes down in PH but the rain water bring the PH up. Its a 200 gallon system all together. 45 gallon fish tank with a raft system of 16 plants of basil and a siphon pump of 500 pounds of gravel next to it. I planted two tomato plants that were all ready 1 foot tall. They arent doing to well. I might take them out.

I cycled the system with pure ammonia without the fish and after two weeks I put in 15 gold fish. They seem super happy and the plants are looking good. Their roots are growing like crazy but the plants arent growing as fast as I thought they would. Does anyone have any suggestions? Is it ok that my Nitrite keeps rising? what are natural ways of fixing the problems? Thanks in advance.

-Zac