The most common substitution is the most literal one, using estar + gerund. All three of your English examples can be translated using this structure.
An alternative, as you already know, is using llevar + gerund. This one would also be correct in your three examples.
- Aunque lleva examinándolo desde esta mañana temprano, todavía no sabemos qué es.
- Cuando decidimos divorciarnos, ambos llevábamos (ya) cuatro años viviendo en Madrid.
- ¿No estás cansado? Llevas caminando desde anoche.
One particular thing with this structure is that it's a bit more loosely coupled than estar + gerund. That is, it's rather common to place other things (complements of time/duration, mostly) between llevar and the gerund. You can do this with estar + gerund, but they tend to keep together.
Yet another alternative involves using venir + gerund, and in some dialects at least, andar + gerund.
These verbs (llevar, venir, andar) have some subtle connotations that differentiate them from estar in this "present continuous". Obviously they connote movement, so they reinforce the idea of the action as an ongoing process.
There's also tener + gerund, which is used only in some places. It means the same, even though the verb suggests permanence instead of movement.
Finally there's a common phrase using pasarse + gerund, which means "to spend (a certain lapse of time) doing (something)". This can be more or less identical in meaning with the "present continuous", or it can be frequentative:
Se pasa los días trabajando. "He spends the days working."
This frequentative meaning is often expressed using a nonsense pronoun (la or lo) with pasarse:
Se la pasa mirando por la ventana.
That means either "He spends all the time looking out the window" or "He goes and looks out the window time and time again". The pronoun doesn't refer specifically to anything, though it can construed as meaning "life" or "all the time".