Hey Barol. I have had this same problem with my engine, except it eventually ran. I had all your symptoms, heavy smoke coming out of the exhaust, long start times, and a delayed throttle response. The only difference is my smoke only happened when I throttled up to harshly, then the exhaust pipe would puke up thick black smoke and black water for about 5 seconds before returning to normal.
What I did to solve this problem was a complete tear down of the engine. I'm sure you were hoping for an easier solution, but the job is easier then you think. All you need to do is expose the valves and the cylinder inside the engine. Your not removing the piston, your not changing any settings. I found that my valves had so much gunk on them they didn't fully close (or close tight enough) and in addition to that, there was rust on the top of my piston. So I cleaned everything with degreasing fluid from Autozone and got the rust off the cylinder and presto! It took hours of work and a shocking amount of crap was removed but the engine fired right back up and ran like a dream. I also added no-smoke (for diesels) to my oil to try and cut back on the exhaust smoke when I throttle up quickly. There is still smoke coming out of the exhaust, because its exhaust, but I don't get any more of that super thick black stuff. The engine was pretty easy to put back together, I just labeled everything and remembered what bolt went where and in what sequence. Not rocket science at all.
I also found that the reason why there was rust on my piston is because the inside of my exhaust elbow had turned into dust. So every time I started the engine, small amounts of water from the cooling loop would backwash into the cylinder. It took some doing but I eventually found a replacement (perhaps the last in NJ) from a Yanmar dealer down the shore.