I also own a '94 Mercury 2 stroke Mercury outboard with the same problem. First, let me explain that this website is a good resource for learning about boat engines. However, you must be willing to make the necessary efforts to resolve your problem. That being said, let me offer the following.
1. If you don't have a good repair manual then download one from this website.
http://www.boatinfo.no/lib/mercury/manuals/45jet-50-55-60.html#/0. Make sure that your serial number falls between the upper and lower limits. You cannot be effective without it.
2. Verify your engine's set-up specs. Carb idle settings, linkage syncs, idle timing, etc. Check it all per the factory manual.
3. I also strongly recommend using alcohol free gas, 90 octane. These early engines were not designed for alcohol.
4. How strong is your ignition. Check your spark intensity using a spark tester on each cylinder while running. Gap should be at least 7/16" and look for any missing sparks. You can get an adjustable one at Auto Zone for around $10.
5. Check your engine compression.
6. Check your gas filters for any contamination or debris. Check your gas lines for any deterioration, cracks, leaks, etc.
7. Check the hoses between the upper and lower scavenger valves. These are located on the top and bottom of the reed valve casting.
8. If you replaced the spark plugs did you use the right ones, check the gap.
One of the primary reasons that you are experiencing this is that your engine could be either too lean or too rich. A too rich condition would result in a lot of smoke when attempting the restart. However, because you are having to use the choke suggests that is too lean. Check your primer bulb to make sure that there is an adequate gas supply and your carbs are full just prior to your difficult restart. If you have not inspected your carbs yet, and they have not had any service in recent history then I suggest that you invest in a thorough cleaning and a kits for all of them. Set your idle adjustment screws 1.5 turns out from being lightly seated. With your engine running in gear under load, (no muffs need to be in tank or on water) slowly adjust each carb screw for optimum rpm. Do not set too lean. My engine will idle for long periods without loading up, (too rich) or spitting, (too lean). I can also run engine at max rpm. and then pull into the idle position without any issues.
This is a lot for a start but sometimes there is an easy answer and sometimes it can be a long way down the list. By the way, I got most of this information from others who are far more experienced on this website. There are other potential issues that you may have with your motor but you should start with the basics. I hope this helps.
