Fire > Cold > Electricity > Acid
To answer your first question, in general, your best bet would be to make your Elemental Metamagic Rod an Acid Rod. In my experience the fewest number of creatures in all the Bestiaries have resistance/immunity to Acid. However, take this with a grain of salt because your campaign setting may be completely different. My experience is with the default Pathfinder setting, Golarion.
The last post of this tread on the Paizo Messageboards (thanks @Lucas Leblanc for the link!) cites a table with statistics from d20pfsrd.com but does not link to it, so take it with a grain of salt. I could not find the original table on d20pfsrd.com. The numbers from the thread are:
- 319 creatures with resistance/immunity to fire
- 305 creatures with resistance/immunity to cold
- 268 creatures with resistance/immunity to electricity
- 258 creatures with resistance/immunity to acid
- 52 creatures with resistance/immunity to sonic (a significant contingient of which are agathions)
- 0 creatures with reistance/immunity to force
As @Lucas Leblanc points out, the differences between those numbers are really quite small (between the elemental types) so what will be most effective for you really depends on your campaign and setting. For example, if your campaign takes place in the north (like Irrisen or Whitethrone), you'll likely encounter more creatures that are resistant/immune to Cold than Fire even though technically more creatures are resistant/immune to Fire than Cold. Additionally, many outsiders (elementals, devils, demons, etc) are resistant to Fire and Cold and not many at all are resistant to Electricity or Acid (thanks @GreySage for reminding me of this!). Rise of the Runelords (RotRL) has quite a few outsider encounters in it, if I remember correctly. I've never played it, but I've read a few of the books and I did play Shattered Star which is kinda like RotRL 2.0 with a lot of Runelord emphasis.
I did find this Google spreadsheet which contains the stats from about 1200 monsters from the various Bestiaries (it may or may not contain all monsters, I don't know) and has a whole tab for resistance statistics. The table is broken out by CR, which is kinda cool. For example, of the CR 1 monsters:
- Fire: 3.70% resistant, 1.23% immune
- Cold: 2.47% resistant, 4.94% immune
- Electricity: 2.47% resistant, 2.47% immune
- Acid: 1.23% resistant, 2.47% immune
- Sonic: 1.23% resistant, 0.00% immune
I also played a Magus who specialized in Electricity but could switch to Acid when necessary, and it was very effective. I never encountered a monster that was resistant to both Electricity and Acid but I would not go so far as to say that a monster like that does not exist.