Is there a technique that would allow me to minimize the time needed to upgrade?

It's very tempting to upgrade to 1.3.9 but due to the large number of customizations in my particular instance, a simple WinMerge process will not work for me. That is, I need to start from scratch and re-apply and test each and every add-on and code customization that's currently on my 1.3.8a operational site. Which means that, for lack of such time and resources, I will have to wait for 2.0 (to go through this HUGE effort only once instead of twice).

Still, I would like to share with you an excellent article that I found in my search for good reasons to upgrade to 1.3.9:

pro-webs.net/blog/2010/05/06/zen-cart-1-3-9-whats-inside/

Through that article I found a thread listing all mods/addons that are compatible with 1.3.9. Unfortunately, most of the addons I am using are not listed there.

If you have a technique that would allow me to minimize the time needed to migrate my operational store from 1.3.8a to 1.3.9f, I would be happy to reconsider.

Never mind the tedious work of comparing PHP files of original 1.3.8a vs. 1.3.9f vs. Add-ons (3-way diff, perhaps even 4 or more) -- as some Add-ons involve modifying/overriding core files.

My main concern is importing existing customers + order information + other Add-on information (such as "How did you hear about us") from 1.3.8a database (+Add-ons) to a 1.3.9f (+ same Add-ons but 1.3.9f compatible).

How would one go about this?

I am sure the upgrade instructions cover very well a scenario of importing pure 1.3.8a database to a pure 1.3.9f database. But what happens when the existing operational 1.3.8a database has numerous Add-ons?

zc_install will take your entire database, as-is, and upgrade it to the latest version.
So, no data is lost. No installed addon settings are lost.

That's why the upgrade documentation instructs you to use the existing database when going live.
It is NOT recommended to selectively pick and choose small sections of data to manually copy from one place to another. Just upgrade the entire database, and you'll have it all.

With many core edits, I have found there is no easy way to upgrade.

DB upgrading is not much of a concern. From 1.3.8 to 1.3.9 I don't think there are any SQL issues.

As for the files, there is no easy way. Winmerge and many hours to spare is the only reliable way. I have upgraded 10 or so sites, and I have always ended up doing manual compares and edits.

Ryan