Did anyone take off the flexible mounts without taking the whole motor out.
they are kinda rusted and need some tlc.
I thinking of putting them on blocks or something.
Do I have to take the shaft off?
Wondering what to expect and how to handle this project.

Stefan - You should check the rubber on the mounts, as both oil and water will cause them to deteriorate, and reduce the isolation properties.

I did it in the water by disconnecting the shaft, sliding it aft and clamping it with a wooden block while I replace the engine mounts one at a time. However...

For best alignment I recommend doing it out of the water so you can pull the shaft and remove the stuffing box / shaft seal to check alignment. It also allows you to check the play in the cutlass bearing. It's cheap to change that out at the same time.

Here's what I used to change the mounts.

1. Put 2x4 long enough to span the companionway opening and have it rest on the deck. I used my cunningham anchored around the 2x4, then attached the other end to a sling around the crank shaft when doing the front mounts, and on the engine center lifting pad for the aft mounts.

2. Unbolt the coupling flange between the transmission and shaft and slide the shaft back so engine can rotate on mounts freely when being lifted.

3. Unbolt the nut on the top of the stud for each mount. Make sure you leave the nut below the engine mounting flange unchanged - you'll need this to preset the new mounts so your rough alignment is correct.

4. Unbolt the engine mount from the boat support frame - you'll probably need 2 people since someone needs to hold the wrench inside the frame cutouts (enjoy the sharp fiberglass edges...).

5. Once unbolted, use the cunningham to lift the engine enough to remove the old mount.

6. Stack the old mount and new mount on a flat surface. Adjust the bottom nut on the new mount so the upper surface matches the old mount.

7. Install the new mount where the old one was removed. Put in the bolts that attach the mount to the support frame. Lower the engine with the cunningham and make sure the mount is centered so the rubber is not stressed in any direction, then tighten the bolts to the boat support frame.

8. Put the upper hex nut on the engine mount stud loosely.

9. Repeat 3 through 8 for remaining mounts.

10. Remove Cunningham and position shaft back to coupling flange - tighten bolts finger tight. Insert a feeler gauge (.010" recommended) in gap between coupling flange and snug bolts finger tight so there is a little friction when you pull on the gauge.

11. Rotate shaft and check that gap is about the same at 90 degree increments. This is where it gets fun if your alignment is way out. If the gap is wider at the top, then the front of the engine needs to be raised and/or back of engine lowered. Keep making minor adjustments on the engine mount hex nuts until clearance is consistent, then tighten the top nuts on the studs. Use a wrench on top and bottom hex nuts so you don't twist the mounts and prestress the rubber.

Ok - that's the ideal world - I found when I removed the shaft seat that the shaft was not centered in the shaft log. I ended up pulling the seal, centering the shaft with the engine attached by loosening the engine mount bolts from the frame, recentering the engine, then redid the procedure above. It worked much better.

It sounds harder than it is. Try it - I replaced the mounts and did the whole adjustment in about 2 hours.

It's probably going to take me a little longer than two hours. But I will give it a try as soon as the boat is out of the water.
I assume you have the older model with the easier access to the engine. I am wondering if the method with the 2x4 will work as well on the newer model.Couldn't you just lift the engine up using a long 2x4 as a lever.
I think I would be able to put a sling around the crankshaft and have a 2x4 on top of the companianway but I don't think I can put the sling more aft.
Now what is the "engine center lifting pad"?

This should work on the older or newer model, as I didn't have the lifting point directly above where the engine was. The key is it's close enough so you an get leverage without any special lifting setup. The leverage with the cunningham is just to lift the engine up - the whole assy weighs about 275#, and you are only lifting a portion of that. I tried the 2x4 lever you mentioned - the cunningham is easier because you can lock it in place with the cam cleat, rather than continuing to apply pressure on the 2x4 lever while you try and turn a wrench.

Go to this link, http://j30rhapsody348.blogspot.com/p/rhapsody-j30-348-yanmar-2gm-rebuild.html download the PDF file on the page, and look on page 5 port side view - the lifting padeye is shown just above the air filter housing between the fuel injectors. If you look at page 14 you'll see my multipurpose cunningham used to suspend the whole engine in my basement! If you don't have the lifting padeye, just wrap a sling around the aft end of the engine. Be careful on the placement so you don't crimp any fuel or oil lines.

thanks for your detailed instructions.
your engine looks great, the new bright yellow oil cap tops it off.