I have recently purchased a 225Hp OX66. It is on a 208 Grady. It runs great and I am really happy with it. I have worked on two strokes for years. Mercury and OMC service technician. I am new to the OX2. There is a lot of information about theses motors online.
Here are a few suggestions that I have.
First and most important check that should be done when changing spark plugs is Compression check. This will give you a good idea if there is a compromised cylinder or head gasket. I found that the top four cylinders are slightly higher than the bottom 2 Cylinders. My engines compression was #1 120, #3 120, #5 115, #2 120, # 4, 120 #6 115.
Spark check tester. I have a pair of Stevens that I use. I set the gap at 7/16" this will load test the coils and ignition system. If it jumps with a clean spark the ignition system is in good working order.
Fuel filters. There are three fuel filters one in the boat screw on water separating, one located under the cowling that is also water separating with a water level float that will lift if water is present and one in the VST. This one if fouled will effect fuel pressure at start up. There is a drain for the VST. Loosen the drain plug with a small catch container and sample the fuel in the bottom of the VST. This will be the best indicator of fuel contamination in the fuel system causing a poor running condition do to fuel. If the fuel that is drained out of the VST is clean and has no water. This is a good indicator that the fuel system is clean.
O2 sensor- The O2 sensor should be inspected and cleaned. If it is dirty it can cause poor running conditions but mostly noticed at higher rpm. It will cause possibly a rough idle.
Low fuel pressure at the high pressure pump may cause a hard start but also poor operating at high speed rpm.
You indicated that the engine performs well at high speed. You can push the throttle and it jumps up. This indicates that it is still hitting on all cylinders.
It is hard to read plugs that have been used for many hours in my opinion. Especially when the engine does not fire on all cylinders at low rpm. The OX2 saltwater idles with cylinder #5 cut out. When the engine reaches 850 rpm to about 2000 rpm #5 and #2 are not firing. All 6 will fire at start up and warm up. If the spark plug that shows cleaner came out of #5 that may be because you do a lot of running below 2000 rpm. This may be true for # 2 also but # 5 doesn't fire from idle to 2000 rpm # 2 cuts out at 850 and up. either one may show cleaner than the rest. This would be normal. The best way to read the plugs is install new and run for a couple of hours then read the plugs.
There is no benefit to pumping the throttle. There is no accelerator pump it is fuel injected.
Hard Start could be has easy has a bad primer bulb check valve. You stated you installed a new one and it fixed he issue and now it has come back. I have found aftermarket primer bulbs suck and fail quickly. I always use OEM primer bulbs. Yamaha, Mercury..... If you used an aftermarket primer bulb replace it with a new OEM.
Low pressure fuel pumps on the Yamaha OX2 are known for failure. It is suggested by Yamaha that this is a maintenance item to to pressure checks on to confirm that the diaphragms are not leaking by. I replaced mine when I purchased the motor. I bench tested the old ones. The engine was running fine but one had a small leak and would not hold pressure. Have you replaced low pressure pumps ?
Brian