spreading out the runs

It sounds like you are following a plan, but keep in mind that those are generalized, and you will probably need to adjust it for your body. I haven't followed one, but from what I understand, most beginner plans (like a C25k for example) will say that if you need to repeat a week or if you are getting injured, then you should. If you need to do shorter runs in order to not injure yourself, then do shorter runs. You might also want to look at you pace. Your long run should be significantly slower than your shorter runs. Increasing distance without decreasing speed or increasing both speed and distance at the same time can lead to injury.

Also, you may want to consider splitting up your long run. I will do this in the summer if it is too hot to cover all of the miles at once. I will do half of the run in the morning, and the other half at night. Keep in mind that total weekly miles are more important than the miles of individual runs. I imagine that swimming is the same way.

It is OK to take things slowly. This should be a healthy process that you enjoy, and it isn't like you are a pro that is going to lose a contract if you don't make it to a specific race.

We would all do better...........adding more run frequency. Anyone just getting started would be smart to do that.

5 three mile runs/wk > 3 five mile runs/wk, IMO

I agree with this! I consider myself a very beginner runner. My biggest week heading into my Oly last month was about 12 miles, as a 6.5 mile long run, and then two shorter runs. That whole summer I was feeling pain in my foot and hip. I've now switched to running more frequent but shorter distances, and it is so much more manageable and fun. I'm still covering the same distance per week, so some of my workouts seem ridiculously short, but I have no pain, so therefore no complains. Listening to your body when you're a beginner is hard, because you aren't always sure what it is saying. I found what works for me is taking pretty meticulous notes in my log, so I can look back on a weekly/monthly/yearly basis and notice trends.
Don't be afraid to take a slower path to your goals in order to ensure that you can succeed at them!

When I first started out on my triathlon journey I dove right in. And guess what? I got a shin splints and a stress fracture on my right leg.

After a couple of months of therapy and rehab I was given the go ahead to start running again, but with the caveat that I start slow and increase the frequency.

I went from running 2-3 times per week to running 5-6 times per week. The mileage stayed the same, but the number of days it took to run those miles increased. Running 2 days at 3-4 miles each day is so much easier on the body than running 7-8 miles in one day. Even now I will split the occasional long run (up 18 miles) into 2 and run 7-8 miles in the morning, then the rest later in the day.

After several years of this I am now back down to running 3 to 4 times per week with big mileage each week. But, it took over 2 years to get to this point. I am over 1000 miles for the season so far. I have ran the Boston Marathon, 3 half marathons, 2 full Ironmans, 2 half Ironmans, and 2 olympic tris this year and not a single running injury or problem. Listen to your body and you will get there and be a better, and more resilient runner.

Thanks, that was what I was hoping to hear. Even at the shortest distances I get this little faint soreness in my knees, I'm hoping it will pass if I go short.

The added frequency with shorter distances should help. You should also consider doing some strength training at least once a week and flexibility exercises maybe twice a week to aid that knee soreness.

Now I'm going to sound stupid but here goes: This is my recovery week and I was really looking forward to moving at shorter distances (too much shorter and I wouldn't be training!).
I'm not at my heaviest so I've been surprised that my knees hurt, probably 2 on a scale of 10, but it's noticeable. I also have a sore muscle by my tricep, I'm assuming because I've just started focusing on high elbow, strong pull, complete the stroke. Used to just windmill my way through the swim.

Do I stop until they pass and start over again or push through?

One thing that has changed is new sneakers. Went to a specialty running store and was shocked at what I looked like running. Major overpronation. It took stability shoes with neutral inserts to get a more normal stride. Assuming these are the right shoes, could a major correction led to initial discomfort or injury?

Really appreciate the feedback.

Mitzi