[MENTION=412307]CPH-Flyer[/MENTION] [MENTION=608317]Tokyoite[/MENTION]
Thank you for the replies. I believe this will help me planning for the long run.
Sounds like I should just pay for standard tickets and not even worry about miles/upgrades if availability would be an issue. It'll be on the back burner for now.

In reply to Tokyoite,
1) I use JAL for the international leg because my final destination is usually Hokkaido and the Japan explorer pass discounts seem to be a savings in time and money after adding in the cost of 3-4 domestic legs compared to booking ANA or JAL domestic at the standard rate after taking a non Oneworld carrier into Japan. I also like the 1pm departure from Boston compared to the 6-8am departures I have to catch for a connecting. I'm also not averse to paying more for things like JAL/ANA premium economy or Jetblue even more space, but business class prices are out of my reach.
2) Mileage run deals likely won't work since I have a full time job and mainly out of courtesy, I tell them I'll be taking 2-3 weeks off for my trips about a year ahead of time. No guarantee that it will line up with a fare deal.
3) I suppose I could redeem my miles I do have for a Wifi coupon and a domestic leg or something instead.
4) I actually was not aware that Asia Miles is Cathay's program. This also sounds like something that is not feasable chasing in the long run for me.