I manually shut off all zones and the pump continued to cycle. So I thought there must be a leak in the manifold section that distributes water to the zone valves. Here's where I was wrong - thinking that it must be something that I put together.
Digging out the manifold (next time I think I should put everything one the surface although I noticed that no one else does) there was a lot of water/mud. However, it was coming from the backflow preventer on the city water control valve. What happened is that the check valve failed and water from the pump/water tank was leaking through and overflowing at the backflow preventer.
I replaced the valve and tried again but the pump continued to cycle. I noticed a drip coming from the zone 4 valve which was manually closed. I pulled off the distribution hose and water was seeping through the closed valve. So I replace this as well and eventually got things up and running.
Lesson learned - don't assume that the problem lies with the part that was manually assembled. As unlikely as it seemed both problems were mechanical equipment failure.