Is this an FRP pedestrian bridge? If so, there are different requirements and your 5 Hz limitation was correct.
If not an FRP pedestrian bridge..... Do you have a copy of AASHTO LRFD Guide Specifications for the Design of Pedestrian Bridges? Refer to Page 7 and 8. They recommend that for the first harmonic (jogging induced vibration) that the fundamental frequency in the vertical mode without the weight of the live load shall be greater than 3 Hz. In the lateral direction, the fundamental frequency shall be greater than 1.3 Hz.
You can isolate your eigenvalue analysis in only the lateral and vertical directions, essentially isolating those modes. You can also run the analysis in combination, however, I would be highly suspicious if your lower modes were not purely lateral or vertical. Typically, combination modes or torsional behavior comes in at higher frequencies with low mass participation (unless it is a long and slender steel bridge).
What is the natural frequency of your lower modes?
When you say the first few modes vibrate only part of the footbridge, what do you mean? If say, you have a 3 span bridge and the middle span is longer then perhaps you will see mostly vibration of the middle span for your first mode. I would not think this is "deemed not applicable." However, if you see an area of your bridge where say a small portion of the deck is vibrating independent of the structure and has low mass participation, then I would say that there is some modeling issues. Typically, I find that if your first few mode shapes don't have high mass participation, it's typically an error with the model. Perhaps boundary conditions are not modeled correctly or elements are not joined correctly. Can you attach a picture of the first few modes so we can see if it appears correct. How are you modeling the foundations? Drilled shafts or spread footings?
If the bridge is pretty straightforward and not skewed or curved, and is on spread footings you should also check the frequencies by hand to see how they compare with your model.