Evidently things have not worked fine…

A have updated my Eclipse and probably also two steps were needed. It has been several years ago, so I do not remember details….

But IMHO you have first complete installation of 3.5 and when completed start update 4.01. It seems to me you have tried to do two steps in one step. And so everything stayed on 3.0.

So,  update to 3.5 and when asked for power cycle, do it. After that you should be on 3.5. Check it.  And repeat everything again with 4.01, if Eclipse is on 3.5.

I do not know about versions of Update Utility. Maybe it does not matter, maybe 2.04 is better. Maybe first you have to use 1.1 and later 2.04. I have used, what was downloadable on Eventide web. Nothing more.