At start-up, all pistons should be working.
If you disable the #1 and 5 cylinders, you are removing every third power stroke. The engine will run quite roughly.
Removing the spark plug is not the best way, because, if you did so, the piston's movement would be shoving air in and out of the hole very quickly. This would introduce frictional losses and fuel-sucking drag due to air pumping loses. Also, unfiltered air would be introduced into the engine, causing excessive engine wear; and it would be very noisy.
The best way would be to remove the intake valve pushrod from those cylinders.... thus the air trapped inside the cylinder would work like an air spring, it would absorb energy upon compression but return it upon expansion.
Also you need to come up with a way of holding the hydraulic valve lifter in it's bore (to maintain oil pressure) but keep it away from the cam lobe (so it does not bounce out.)
Also, you would have to unplug the appropriate spark plug wire and fuel injector.
Doing this would give the ECM fits. You would get the 'Check Engine' light on and the ECM would throw several codes.
The car would be SLOW.... imho slow enough to be dangerous and unusable for highway driving. The engine would have less power than a V4....... due to the excess frictional drag of 2 extra cylinders. It would feel more like a V3.5
Frankly, this idea of disabling cylinders for better fuel economy has been around for decades. I have a 1981 Cadillac (parts car) with such a system..... and mine worked very well, even though these engines developed a bad reputation.
Several new cars use such systems these days with great success. However, these cars all have the ability to reactivate all cylinders very quickly when full power is needed. Your idea would not allow this... leaving your car (imho) slow, unsafe, rough and miserable to drive.