Fibular head pain is often from over-straining one of your hamstrings. Often, this starts because of a seat that is too high and/or too far forward, but occasionally, it can be strained by a seat that is too low. If that's not it, I'd consider moving your cleat farther back on that side. The cleats should be such that the first metatarsal joint is a bit (usually under 1cm, often closer to 5mm, depending on your foot size) in front of even with the pedal spindle.

SPD pedals can be adjusted to where your toe-in or toe-out position is more natural by rotating the cleat itself on your shoe, though road pedals with float will allow some more wiggle room for your pedal stroke and can eliminate hot spots, improve power transfer, etc.

Another thing to consider is that you are just new to clipless pedals. This means you're pulling up more than you were before. Even with toe cages, you can pull up better and with slightly different mechanics with clipless pedals. So you might be engaging the hams more and have just strained something. Massage the hamstrings well. Stretch well. Use some muscle rubs. You may find that your fit really isn't that far off, but once you've started straining something, it can continue to bother you for a while. Fibular head pain means you've probably pissed off the biceps femoris tendon which will take longer to heal than just wearing out the hamstring itself.