Re: 1999 mariner 40hp 2 stroke pull start engine into gear thud.
Shouldn't. The prop should be tight on the shaft. Actually for my 90 hp the torque is 55 ft-lbs. For yours, maybe 45-50....50 is not a lot....you can get that holding onto the prop while turning the nut till you can't hold onto the prop any longer. If the prop is loose, there is your smoking gun.
On the prop shaft of my engine is first a thrust washer, tapered inside to fit the taper on the shaft. Then the prop. Then a big washer with tab slots in it. Then a SS sheet metal tab with 6 ears on it, then the nylon inserted nut. The process is to install all that and as you are tightening the nut, align 3 of the tabs with 3 slots in the washer while also holding the washer against the back of the nut so that the hex detent in the tab fits around the hexagon shape of the nut. I put my knee against the prop and use one had to guide the tab'd washer. Then torque her down and as you are, stop when you get 3 tabs and slots to line up....at the torqued value and bend them down to lock the nut.
On smaller engines like yours, you MAY not have the additional locking feature of the tabs......but you do want the nut tight.
I was thinking about this thread last night on the way to sleep and one thing occurred to me. When you shift out of N, how far do you advance the handle? Since the handle is dual purpose, if you push it too far too fast, you will increase your rpms before you want to. Doing that can cause a thud.
HTH,
Mark