"Jack...What is your serial nu
"Jack...What is your serial number on the frame? i'll check to see it the warranty work is in the records.
Also, if you have not done it already, I would go to honda-marine.com and click on owners link, then product registration. Under registration about the fourth line down you will see "If you need to change your name, address, phone number or ownership information, please click here"...you can then officially transfer the warranty of the motor to you. That way, you can be notified if issues arrise in the future.
More basics...
1. Check Oil - make sure it is not too high.
2. Check PVC valve (yes this motor has one) See your shop manual
3. Check thermostat to be sure that it is not always in partially or full postion. Then engine would run too cold.
4. Check timing marks. Since you have a shop manual, you may want to check to be sure that the timing marks line up. You can find this in the maintenance section under valve adjustment. Make sure that your timing belt is tight. It has a self tightener. If the belt feels real loose, it may have jumped timing.
I'm trying to go for the easy stuff first.
I am also assuming you are using NGK spark plugs and a good fuel treatment like Sea Foam, PRI-G, Quickkleen, etc.
The intake breather is actally called a silencer. I wouldn't run long without it. It definitely will be more noisy. I can not confirm its other functions at this sitting. While we are talking about it, there is a small plastic hose that attaches to a nipple on the bottom. Make sure the hose is not plugged up and make sure the other end goes to a spot on the bottom of that area that is a hole to allow air for it to breath. It should not be connected to anything else.
Eventually, a leak down test would be good. Hopefully, you will find one of the "obvious" things.
It is really hard suggesting rational things to do without seeing the engine. If I think of some other basic things, I will let you know.
It may be possible that there are cracks in your head. Even though it was replaced before, there have been some issues with these depending on your serial number. They cause idling and acceleration problems. I am not sure what the spark plugs would look like like. The ones I ran into, one cylinder failed and there was water on the spark plug. Unfortunately, the head will have to be pulled. That is better done by a dealer. Also, if there are cracks, it may still be covered by a 10 year (from original purchase)warranty. This is assuming the unit was purchased in the United States. The warranty only applies if there are cracks around the water passages. Anything else, you are on your own. There are several other things that could go wrong with the head...hope it does not get to that."