The Invader is an amazing sled. Clearly the performance you are seeing is not what this sled is fully capable of.
There is no way to fully know the condition of the engine. The fix, while simple, may take a while to sort out from all of the many factors that can affect sled performance.
From what you have said I am suspicious of two things, the carbs and the clutching.
The sluggishness suggests to me the carbs. And the topping out at 40 suggests clutching.
I would suggest a thorough carb cleaning and new jets. And, I am not a wizard with clutching, there are others here who can give you better advice on clutching, but recently we found that a number of our sleds, because they sit so much were not allowing the secondaries to open. Just polishing the jackshaft on one Intruder found us an additional 10 mph! And I think that there is a little more that she can do if I work at it.
So at the end of the day you probably have a number of little issues that are adding up to the observed performance. The really good thing is that she runs and you know that you have spark.
Also, I am assuming that you are using fresh fuel. They never run right with old fuel.