'Couch to 5K' to '16 Wk Oly'

Try a build week on the shorter runs at a higher intensity. Basically switch from Volume to intensity. keep your long run on a very even heart rate, maybe Top Z2 max, or wherever you are now.  

 I did sprints last year and am aiming for Capital of Texas Tri on Memorial Day here in Austin - after coming off a half marathon training program  - I could easily do the longer runs, so I ramped up to my 5K pace on the shorter runs and when I go long, I just keep it low and slow.  Tell me if/how it works for you.

You're decreasing running distance and volume, but adding cycling and swimming. The thing to look at is overall volume. If you've been running for 120 minutes per week and suddenly add 180 minutes of cycling and 120 minutes of swimming, you're putting a lot of stress on yourself. Decreasing the run volume initially can help to ease that. 

Something else to bear in mind is that cycling and running do use some of the same muscles. You can aggravate some running injuries by cycling and vice versa.

Have you considered changing intensity rather than volume? Say, doing the long runs at Zone 1/2, and start to add in some speed or strength work on the short and medium runs. The added intensity will more than make up for the decreased volume.

If you're concerned about performance on race day (you train to race), you'll get more out of doing each workout with a specific purpose in mind. However, if you're training for general fitness and a goal race helps to motivate you (you race to train) do the runs that you enjoy.