He had so changed that I no longer recognised him
This sentence seemed strange to me at first. Why? Because you use the adverb so to modify the past participle changed, and split the combination "had changed". The past participle changed here is tightly linked to the verb had, they are used together to put the clause into the Past Perfect tense.
But I found these modern uses of this construction:
Evan Richardson, 2013: "My life had so drastically changed, and I myself had so changed, that seeing this old tribe at the Pierre was like a bad trip back in time that no longer applied to me." (Here we have so inserted between had and changed, just like in your example).
I looked in Google Books for had so much changed, and found several quotations from the 19th century:
The Indians now had so much changed their deportment as to bring in horses or cows, that they found astray from the mines. (Here, the adverb so much splits the Past Perfect construction "had changed"; but here the verb is used transitively: it has the object "deportment", and maybe this makes the split look more natural)
Your first sentence looked more "natural" to me:
He [had changed] so much that I longer recognised him.
Here, we are using the adverb so much to modify the whole "verb combination" had changed.
So, it is not an error to put something between a verb and its "helper". I found an interesting little article in The Economist, here's a quotation:
I didn't realise that quite so many people consider it an error to put anything between a verb and its helpers like auxiliary verbs. To this crowd, "We have always been friends" must be "We always have been friends." This is, of course, a rule that would subsume the so-called ban on split infinitives, the rule that declares "to boldly go" an error. Prof Liberman and the commenters have a roundup of the usage manuals that prescribe this false rule. One source says that the rule is "widespread among newspaper journalists", which comes as a surprise to this practitioner of the hackish arts. The Economist has no such rule, though we do tell journalists to avoid split infinitives because they annoy so many readers.