If you have enough Calcium (Ca) in your wort, the pH should drop to 5.1-5.2pH during the boil, it will drop further during the ferment to about 4-4.2pH. Given you have enough Ca you should in a 90 minute boil be getting close to the target pH.
On the layout of your plumbing, a picture might help but you should be able to work out a better pickup height, somewhere around 1/3 of the wort height from the bottom would be ideal. Maybe a new hole and bulkhead will be required, if you want to keep using the counterflow the way you are.
Running wort as it cools through a pump is problematic; the textbooks say to keep the flow rates/velocities under 3m/s, very good chance your pump impellers are going a lot faster than that.
I would be tempted to whirlpool at the end of the boil having added your kettle flock with a spoon or paddle then draw down the wort through the counterflow chiller, slowly enough to allow it to cool on the way to the fermenter.
A syphon or gravity flow would be better than pumping.
You will still get some cold break but that isn’t a problem, it’s the hot break you want to leave in the kettle.
Mark