Medina Azahara, is it worth the trouble

Depends on what sites in Andulacia you wil be doing. On a 3 stars level, I’d put a 2. We were not totally wowed but we enjoyed the time we spent there.
It’s easy to walk
If you have time do it. If it makes you miss important things in Cordoba or elsewhere, then skip.
Close, another spectacular site is Almodovar del rio castle. I think we enjoyed this site more. Spectacular views from above.

I don't know if it's still offered, when we were there the Cordoba tourist office sold tickets that included a direct bus to the complex, entry and a bus back (no guided tour). So for us, with several days in Cordoba, it wasn't any "trouble" (and we'd already seen a lot in Cordoba itself).

I liked the place, although it is mostly ruins with some structures including distinctive Moorish arches, but mostly what you see is at low/ground level. It's an interesting contrast with and supplement to, for example, visiting Alhambra or Sevilla's Alcazar - but not an adequate alternative to them. I thought it was rather atmospheric to see this once vast & important site of power (what you see is about 5% of the original palaces and administration centre), had now crumbled (or been stolen), away. A useful warning against modern-day hubris too, perhaps.

If you do go, take water, etc. as it can be hot, un-shaded and dusty. In answer to your second question - the modern museum is at the bottom of the hill. A shuttle bus then takes you to the top but from there you need to walk back down a moderately steep path (then back up at the end, of course), to get to the ruins. Within the ruins, some parts you walk on the original floors, but others on unmade paths, but it wasn't particularly arduous