... you can't present perfect (or continuous) and past simple within a sentence.
As it stands, this rule is incorrect. In many cases it is acceptable and logical to mix past and present references in consecutive clauses
I lost my keys last week, but now I have found them.
This makes sense: A was true then, but B is true now.
This, however, does not make sense:
He has decided to go hiking, so I went hiking as well.
This sentence amounts to A was true then, because B is true now. The simple past describes a past event, your going hiking, but what the present perfect describes is not a past event, his decision, but a present state which is the result of a past event--his state of having decided. That present state cannot be the cause of the past event. The cause must be either a past event or a past state:
He decided (event) to go hiking, so I went hiking as well or
He had decided (state) to go hiking, so I went hiking as well.
The important thing is not to mix time references illogically.
As for the sentence in your friend's email:
Getting that email was such a pleasant surprise, because I was just thinking how I've been wanting to send you an email
There is no mixture of time references here, because the progressive construction "I have been wanting" marks a state, not an event, which may very reasonably be taken to continue into the present out of a past which is marked (by "just") as immediate. In effect, these pasts inhabit the same time frame as the present.
In any case, the "rules" are very loosely applied in informal discourse; see my discussion here. A casual email, which your friend probably dashed off in excitement, should not be held to the formal literary standards of coherence.
To begin with the active sentence is not strictly grammatical. It needs to have I have or an it's between and and not. But that is not particularly important as it doesn't affect the main point.
Neither of the passive suggestions are fully correct.
It should, in my view, be He has been being told a long story by me and it's not finished yet.
Best Answer
The idiomatic use of the word "with" in "visit with" has changed the verb from a transitive to an instransitive, thus also restricting it's meaning to "socialize with," or "go and socialize with." It is not strictly speaking functioning just as a preposition, but part of the idiom of what goes with the verb visit, as well as some other verbs. In this sense, "with" doesn't always adhere to usual grammatical prepositional use, since it is really part of the verbal idiom.
Visiting with/ Talking with/ Eating with/ Drinking with/ Dancing with/ Going with/
All of these are taking the preposition "with" but as part of an idiomatic form of meaning, here also typically intransitive. Contrast this to a different use of "with" where it is not an integral part of the verbal idiom. "The girl ate her ice cream with great gusto." This with is not part of the verbal idiom ate as ate took the direct object , and with explains in what manner she ate the ice cream. I hope this helps explains the difference.