Hi Linda. Thank you for your question. I am happy to help with diagnostic and repair advice.
This sounds like you have either a mechanical or fuel related problem. In PWC diagnostics, anytime there is a running problem, especially on the 2 stroke water craft, we always start with a compression test.
I would like you to do a compression test on both cylinders please. You will need a compression tester to do this. Also, when you do the test, make sure you only remove the spark plug out of the cylinder you are testing. Do not take both of them out. Also, make sure you ground both spark plug leads. You can use the spark plug you took out of the one cylinder to install in one of the plug caps and then just lay the metal part of the spark plug on the cylinder head. You can use an old plug for the other spark plug cap.
If hte compression test comes back good, we are going to have to take a look at the carbs. That is going to include taking them apart. Are you comfortable doing that and have all the basic hands tools to get them off and apart? There are no special tools required, just basics like combination wrenches, screwdrivers, side cutters and basics like that.
Let me know where you are at on this.
As far as that hesitation you felt, that is a lean condition on the low speed circuit in the carbs. We can fix that later because that is not the cause of the black smoke you have pouring out the exhaust now.
Also, Yamaha made 2 RA700's in 95. One was a had a purple hull with an orange seat, the Deluxe had a blue hull with a yellow seat. Which one of those do you have?