Is it lack of motivation, over-reaching, something else, combo? HELP

It'll pass.  Fight through it as best you can.  What you describe sounds as much mental as physical. If it ever gets into the exessive soreness category then of course back off.  Otherwise, sounds like a normal mental challenge post-illness with perhaps some post-illness gunk you gotta work outta your system.  Common.

Of course, this is my opinion based on your post.  Actual results may vary.  Consult actual excperts for details. 

I think the weather has a lot to do w/ it.  We s/b running in shorts instead I was wearing friggin gloves last night. Hang in there, the first 70 degree day you'll be playing hooky and running a 5k.

Or you can come join me at Harriman tomorrow. Nothing like an arse kickin on the hills to motivate you to back into the saddle.

Do your favorite workout. I know you are supposed to work on your weakness, but you need that good feeling.

As far as your breathing, go to your doctor. I know it feels ridiculous for a small nagging ailment, but I went yesterday for breathing problems and I had to explain that I can breath fine just sitting around, but taking a deep breath is difficult and a little painful. To my surprise the doc took me very seriously. Turns out I just have reflux, never in a million years would I have thought that! But the doc had plenty of ideas to check for.

Many people are having allergy issues this year, even people who don't usually have seasonal allergies.

Whenever I get sick, it takes me a couple of weeks after getting "over" it to really be over it.  I expect that once I start feeling "not sick", I'm still probably only at about 60-70%.  It can take me up to 3-4 weeks to get back to 100%.

Which is why I'm really freaked out about getting sick.

I'd say keep working out, but also make sure you're getting enough sleep.   You body does most of its healing/fighting when you're sleeping, and you don't want to get in the way of any clean-up battles it's fighting to keep you well, right?