I am nowhere near a pro but have read a lot. I wish I had the experience...
I am experiencing the exact same thing. Went out today intending to run 8-9 miles below 155HR and immediately went above 155 if I ran below 9 minute miles. It is frustrating. I think your question about the programs is a good one and I think they may structure the bike with the swim just due to time constraints as if you did a long bike ride and swim in same day the time load would be too huge that day. If you do run and swim in same day, you are looking at only 2-2.5 hr day, a reasonable day.
You can start a base phase now and can pick a 12-16 week training plan. I am in the same boat and trying to figure out if I can do a half Sept 7th and am looking at a plan Matt Lieto had on this site also that is a 20 week plan. I would appreciate any advice on half ironmans as well. Anyone have a recommendation for a trainer or plan they have been very happy with? Good luck.

well, there are a lot of questions in here but I'll try to speak to some of them. I'm no pro either but here's how i view things and what's worked for me.

Basically, yes you have to go slower to get faster. That's the theory behind going slow in base and building a solid base over many years of training. You basically want to learn how to go faster while spending less energy. To do so, you need to be training at that lower heart rate and slowly build up your speeds. So that after going through the cycles of training with base and the lower heart rate/effort theory you'll be able to run those 7:30s at 140bpm. It has worked for me. It totally sucks running 9 minute miles or riding at 17 mph when you know you can go faster, but as the years go by you begin to understand the importance of building a good base. Easier to get back into the swing of training after the off season, easier to maintain long efforts, eventually you will get to 7:30s at the same effort you were doing 9's. And as you get older, recovery is easier if you aren't going anaerobic all the time.

I don't do any speed work during base. However people are changing things up a bit. I know pros that do incorporate some harder speed efforts during base. But, they also have years of base behind them so their fitness is there.

the swim/run vs. swim/bike is basically due to time for training as mentioned. typically easier to double up a swim with a run. Although usually not back to back. As you get further into your training plan you'll typical incorporate some bike/run bricks to simulate the transition during a race.

I use Matt's plan as a basic starting point and taylor it to my specific schedule and where I need more work.

Some links that might help:
http://www.trifuel.com/training/heart-rate-training
http://www.trifuel.com/training/triathlon-training/what-does-periodization-mean-and-how-does-it-work
http://www.trifuel.com/triathlon-training/Half-Ironman-Training.php

Thank you tribro and Jellings. I think I will get my zones figured out from testing as this seems best. I will use Matt's plan and just go with it as I think getting on a specific plan will help a lot. Right now just doing a lot of training without much improvement. I do have a powertap so was thinking of a power based plan but seems like that is unnecessary at this point.
Thanks again.

I switched from running by HR to running by pace.
Reason is because your HR can really fluctuate day to day based on so many things: stress, hydration, recovery etc
I used the Jack Daniels formulas to base all my run paces from. Essentially it has you run an all out 10K. Plug in those numbers and from that time it derives your long run pace(Z1), marathon pace(Z2), half marathon pace(Z3), tempo pace(Z4), and interval pace(Z5). As well as a pace for whatever race distance. Then you just run that pace as prescribed in your training plan.
You stay with these paces until you test again with another 10K (4-6 weeks later) and adjust the paces accordingly.
I've been seeing pretty good improvements this way.