Learn English – How to parse “once upon a time”

I think you see the whole thing totally wrong.

A direct object never has a preposition.

• I'm reading a novel - a novel is a direct object. You ask: What am I reading?
• I'm waiting for the bus - for the bus is a prepositional object You ask: What am I waiting for?

In your sentence "Pilgrims learned about planting crops from the Wampanoags." "about planting crops" is a prepositional object and "from the Wampanoags" is a second prepositional object.

Maybe English grammars have other terms, but that's the way I see it.

We went swimming later in the afternoon, Jack and I

This sentence has been done something to.
It's an example of the syntactic rule of Right-Dislocation.
The sentence it's transformed from is

• Jack and I went swimming later in the afternoon.

The rule copies an emphasized Noun Phrase (which may be subject, object, or oblique) in a sentence, and repeats it, with a different intonation, for emphasis, at the end of the sentence. It's not a movement rule, but a copying rule, since the original NP remains in place as a pronoun.

There's also a rule of Left-Dislocation, which copies the NP to the beginning of the sentence.

Here's the entry from Haj Ross's list of The Top 200+ English Transformations
  (p.4, categorized under "I. Emphasis; A. Pseudoclefts and Dislocations")

"6. LEFT AND RIGHT DISLOCATION:

• My horse snores. ➞ My horse, he snores. (via LEFT DISLOCATION), or

• My horse snores. ➞ He snores, my horse. (via RIGHT DISLOCATION)

In pseudoclefts, this rule will produce related sentences like the following:
Anne's brother left ➞ Anne's brother is the one who left ➞ Anne's brother, he's the one who left."

Some more examples of dislocated sentences:

• My Uncle Will hates the Dodgers a lot. (Base sentence)
• My Uncle Will, he hates the Dodgers a lot. (Left-Dislocation of Subject NP)
• The Dodgers, my Uncle Will hates them a lot. (" of Object NP)
• He hates the Dodgers a lot, my Uncle Will. (Right-Dislocation of Subject NP)
• My Uncle Will hates them a lot, the Dodgers. (" of Object NP)

As for why anyone would think any of these are more or less "formal" or "old-fashioned" than others, I can't really say. "Formal" and "old-fashioned" are not linguistic terms, anymore than "fad" or "fancy". Everybody has their own idea(s) about these terms.