I needed a base gasket, head gasket, water cover gasket, thermostat, thermostat gasket, and the upper water grommet (there are two, inlet and outlet). You may need a new spring for the thermostat. If you mainly boat in fresh water, the spring will likely still be good, if you do salt water I would buy a new spring.
Take good notes and pictures (if you have a digital camera) as you go and before you start, it will come in handy for reassembly.
Reference this site too:
Maintaining Johnson 9.9 Powerhead/Gearcase Leroy give detailed info on how to pull the powerhead. Especially if the base gasket is stuck.
Remove the lower unit.
To pull the engine, remove the mixture needle from the carb, makes pulling the air silencer easier. Remove the choke knob, and air silencer. Pull some rope out of the starter (about a foot) and use small vise grips or tie a figure 8 in the rope. Remove the starter bolt and pull the starter. Hold the starter together and either tape it together good with electrical tape or use an appropriate size nut to hold it together, I think it's a 5/8 nut.
Remove the fuel pump, and pull the fuel line from the carb. Remove the throttle linkage and disconnect any wiring in the way. Remove the power pack, and the ignition coils. Disconnect the tell tale from the lower cowl connection.
Now you should have everything out of the way to pull the engine. There are 7 bolts underneath the lower cowl. Remove those, will be difficult if they've been exposed to salt water. One will remain in place, because the tiller mount prevents its removal.
To remove my powerhead, I used a thin metal scraper blade to separate the base gasket as much as I could. I then took the whole motor out to my yard, held it a few inches upside down by the lower cowl, and shook it loose from the midsection. Once it's out, remove the exhaust pipe and the grommets are right there.
I also pulled my cylinder head off, and took the water plate off too. I used a dremel to clean out the entire water jacket (mine was a salt water motor before I got it). Replace the thermostat while it's open too, really easy to do while the engine is off the midsection.
Replace the grommets, gaskets, and thermostat. I used Evinrude triple guard grease on all bolt except the cylinder head bolt threads (needs proper torque). I greased the smooth shank/unthreaded part of the cylinder head bolts, thats the part that tends to corrode and get stuck. Take the opportunity to clean out the lower cowl and other inaccessible areas on the motor. Reassemble the engine.
When you water test the engine, do it in a barrel. You want to make sure that the water pump is able to do it's job and keep the engine cool. Ear muffs are great for flushing and test running, but not for diagnosing cooling problems.
