Cracks on the boots can create a lean condition and that could definitely cause issues. I would check compression. If the cracks have been there a while, the engine may have sustained damage, which caused the low compression. Check it to rule it out.
Compression should be over 120, with a good engine maybe even as high as 140-150. Compression difference between cylinders should be less than 10%. An engine may not run well at all and may not even start with less than 100 psi compression.
I can't see the plugs well enough in the pic (it does not expand) but your plug color should be a cardboard brown. Black would indicate too rich, white too lean. Grey may indicate a transfer of aluminum from the piston onto the porcelain of the plug electrode, especially if it shows spots of metal.
Don't use starting fluid, pour a little bit of gas down each cylinder most use gas with 2 stroke oil in it say for a chainsaw or weed trimmer. Starting fluid was made for diesel engines not 2 strokes. Did you clean every single jet with a small piece of wire? After that try cleaning or replacing the fuel pump. Look into the gas tank and make sure the fuel line hasn't rotted off either. Hopefully BearAK can pop in as he is the go to guy for Ski-Doos, good luck.
Sounds to me like you still have issues in the starting circuit in the carbs... try cleaning again, paying particular attention to the pilot jet (the one up the tube) and the air and fuel passages that lead to it. You may have to shove a small soft wire into the passages to dislodge any crud that has grown in there over time. I use a strand of Cat-5 cable with the insulation on to do that. The pilot jet can become so varnished that it becomes smaller than designed, so poking a wire through there may help "floss" the jet to clean out the varnish. I've had to go through carbs as many as three times before they were clean enough to run properly, especially if gas with alcohol was used. That stuff is horrible on carbs that sit a lot.