Megasquirt EFI Lean Cruise Reality Check

I don't think you have a rotor phasing problem, as you say WOT is 'fantastic'.
I know nothing about MS, but it sounds like cruise is simply too rich. Too rich burns slowly & mixture could still be combusting when the exh valve opens...which gives popping in the exh. If the injectors are leaking [ faulty, pressure too high? ], then on decel the higher vacuum will pull fuel from them for an over rich mixture....& you know the rest.