Re: Fishin motor --not a space ship
1. Ventilation is sucking air from above the water (or out of the exhaust when in R). Cavitation is causing "boiling" cavities of water on the suction side of the prop. Totally different things. Your 9.8 is very very unlikely to suffer from cavitation. If you trim incorrectly, or are jacked too high, you could ventilate.
2. Shaft length and transom height work together. Shaft length is measured from the underside of the transom clamp (where it sits on the transom) to the antiventilation plate (the big plate just above the prop). That is typically rigged to be about even with the bottom of the boat, +/- an inch initially. Then trials from there find the sweet spot. Modern Japanese motors are longer than older motors, sometimes about 2" longer.
3. Proper rigging of any motor of any brand on any boat requires centering, correct height, appropriate trim, and correct pitch for the application. These primary parameters must be the best in order to get the best overall performance. Small motors (especially if a bit undersized for the boat, as in your case) can benefit a lot from proper rigging. It must be done on the boat, in the water, and the sweet spot located by trial.
4. If you must have the boat go slower than the minimum idle speed (which needs to be confirmed with a good shop tach... and is about 950 for your motor -- do not set it below that, or there will be other problems), then you need to go with less prop pitch (or run one of the 4-blade HT "sail" props)... so that the idling motor creeps slower through the water.
Note: Beware that if you are severely under-propped (to go really-really slow at idle), you can exceed the max WOT RPM. In the case of the MFS9.8A3, there is an ESG (electronic speed governor) that will engage at about 250 RPM past the max... The ESG will stagger ignition to prevent you from over-revving. So... If you are under propped, when you get to full throttle, the motor will complain with staggered ignition (and will definitely sound like it is "stuttering") to prevent it from blowing up. That's pretty easy to identify... if you have a tach, you will be at about 6200. Even if not, easing back on the throttle a little from WOT will get rid of the stutter.
5. The "pain in the neck" comes from not knowing how to rig the motor -- any motor. And there is plenty to know... hence professional boat riggers. That's where, if you get stuck, a local pro can help. What does your dealer have to say?
6. Yes, it is possible that your transom is too short for a given motor. In that case, shimming won't work, and a pro will need to make a modification. We see that a lot, when long-shaft motors are run on short transoms. If it turns out to be a matter of a boat with too low a transom, none of the modern motors will rig out correctly without transom modification.
7. Running the carb dry is standard procedure. It was always a good idea. Today, it's mandatory, if the motor will sit for more than a few days. It's a good habit to get into, since a couple of days can turn into a couple of weeks. Modern EPA-rated carbs are more succeptible to varnishing from the evaporation of fuel, but the real culprit is that today's pump gas is very dirty, and laden with alcohol and water... none of which are your friends.
Since the Tohatsu motor is also the Nissan... and the Mercury 4-stroke (30 hp and below)... and the Evinrude 4-stroke (20 hp and below since 2012), there should be a dealer in your area who can assist you in rigging your setup. For that matter, brand familiarity is not critical to the rigging. The principles are the same regardless of brand.
HTH