If you are content with your current pickups and dual volume pots, you might be wiser to buy the STC-2C-BO Blackouts for Bass EQ (dual concentric, stacked pots version) or EMG-BTC.
How generous is the neck position pickup cavity of your bass? Is it cut tightly to the outline of the pickup or is it rectangular and big enough to take a "soapbar" pickup?
The PCB might have to go in edgeways and with the velcro trimmed down by a few mm.
A-ha. I see that you are left-handed.
The schematic diagram that you followed for your new pickups was right-handed. This might explain why your controls are misbehaving. Any chance of a photograph of your control wiring, please?