First of all....the 90 design has been around since 1996. There have been a few refinements along the way, but overall a very good engine. It started out using a Mercury lower unit. The 2001 has the more current lower unit....made by Honda.
There have been a few issues over the years, but nothing major.
-Have the owner do a compression test in front of you. Should be in the neighborhood of 213 plus/minus 14 psi.
-Have the owner start and run it on the stand. While it is running, have him do a cylinder drop test. He should pull spark plug wires off of the spark plugs, one at a time.....the engine rpm do go down slightly with each wire pulled off.....about the same on all cylinders. This lets you know that all of the cylinders are indeed firing and it is a pretty good chance that the carburetors are clean. You will not know for sure that all is well until the motor is on the boat with a correct propeller.
-Of course check the oil and gearlube. Most likely, they have already been changed...so it probably will not tell you much. If the oil is black, make sure the owner changes the oil, filter and gear lube before the sale.
-Find out when the impeller was last changed. If the seller does not know, have them throw in a impeller change, if you can. If not, then if you purchase it, make the impeller change your first maintenance item.
-If this motor has been used in salt water, ask to see the thermostat. It is easy to get to and the thermostat and the housing will give you an indication of any potential salt buildup.
-Next...who is going to install the motor? If the selling is.....make sure that he watertests the boat to be sure that the proper propeller is installed. You should also make an on water demo part of it, so you can be sure that it operates properly....and operation is properly explained to you.....especially starting. This motor should start right up (in a could of seconds) if you put the shifter in throttle only....advance the throttle about half way or so and hold in the choke while you crank the engine. When the engine starts, reduce the throttle to a lower rpm. The motor will sneeze and cough at first....you might have to push in the choke momentarily to keep it going at first. When the motor warms up, it should not do any of the sneezing or coughing. Once warmed up.....to start, you should just turn the key to start.
-When on the water, you should be about to get the motor to about 6000 rpm with the motor properly trimmed. If you are a little above it or pretty much lower, have the seller change the prop.
-If you are doing your own rigging, then you are going to be the responsible on for proper engine height, cable running and connections, and proper prop size. You might be able to work with the seller....if it is a Marine shop, to exchange the prop if need be. It may not be an even exchange, especially, if he has to order a new prop vs the used one.
Everything is negotiable.
I know there are many other things to consider....just too late in the day to think of them. Hopefully, others will add on more intelligent items.
Oh! One more thing.....if you are in the USA, you can check on relative engine prices at the following website.
http://www.nadaguides.com/Boats/Outboard-Motors
Hope that helps.
Mike