Grammar - Having known subject for X years, I am sure that

The phrase having known him ... is a participle phrase modifying the subject of the main clause, I. This construction is perfectly fine and is often used.

It could be reordered to

I, having known him ... , am sure that ...

This alternate construction is a bit clumsy because the subject of the sentence is separated from its verb by a very long phrase. There are various alternatives such as using a compound sentence

I have known him ... , and I am sure ...

or

Because I have known him ..., I am sure ...

Having studied English for more years than I care to remember, I am sure that the construction is entirely acceptable. More than 10 years since we were at the same school might give a stern critic pause, as being at school isn't a point in time but rather a period; since we met at school might be better. That, though, is a semantic point; there is nothing wrong with the construction of the sentence. It does have a formal sound, but if this is some sort of reference that is all to the good.

Your suggested replacement is noticeably worse than the original. At present it is a comma splice, trying to cram two sentences into one and so not having an identifiable main verb, subject or other required components. If you replaced the comma before I am sure with a semicolon it would be grammatical, but lose the causal relationship.