My feeling is that either that spark to cyls 1 & 3 is no good; or the injectors at those cylinders are sticking open/leaking large amounts of fuel. The thing is to know how the fuel program was set up so you can know at what % off idle the second set comes on line.
See with the OE system at idle if the car behaves like yours you could say with a high degree of certainty that the primary injectors at 1 & 3 are stuck open or/and leaking fuel. With the secondary delete i don't know enough to make a stronger statement than I suspect that those injectors are fubared or those cylinders are getting no spark.
Tom