I have similar (apparently block-size-related) problems (on a Windows XP PC/Workstation) and a Windows 8.* laptop. I have been using a USB-to-SATA adapter for years, cloning disks for backups. It appears that the way WD implemented 512e (Advanced Format) for dealing with compatibility issues w.r.t. 4K blocks renders USB-to-SATA adapters pretty-much useless. Such disks report a virtual block size and a physical block size, but the API-like functions seen by the O/S via the adapter (and driver) seem to report a “block size” of 4K for 512e disks.
There are rumors on the web of the ability to change the block size, but they seem to be in the realm of urban legend right now. I noticed somewhere in the Acronis documentation that, to clone a laptop disk (using a USB-to-SATA adapter), you have to remove the disk from the laptop, attach it via the adapter, and put the (blank) destination disk into the laptop. You run Acronis True Image off of a DVD and copy from the external disk to the internal one. [One benefit, I guess, is that you get to test the copy by booting it.] I haven’t tried it, yet. This is something to try. I bought five disks that are identical to the one in my laptop (running Windows 8.0).
Using the USB-to-SATA adapter, I used Macrium Reflect (installed on the laptop, with the O/S running) to clone the (running) system disk (all partitions, including UEFI and some brand-specific and recovery partitions) to two external destination disks. I put one of the two copies into the laptop and booted it. (No problem.) Then, I upgraded to Windows 8.1. Now, the internal disk (which is a copy of the original one, but upgraded to 8.1) shows up as having 512-byte blocks. (Makes sense.) BUT, the other disks (including the one that was cloned from the SAME 512-byte original disk) now shows up as having 4K blocks (which means that they can’t be used as clone destinations, at least with Reflect and via the USB adapter). So, Windows is also a part of the problem. (Worked fine in 8.0; doesn’t work in 8.1.)
As for your problem, I would try the “reverse clone” method recommended by Acronis. [And, please report back here.] The Acronis documentation does not say why it works (and I haven’t been able to get any information by contacting them about it. And, they don’t say that a “forward” clone won’t work (which is what people are experiencing). Instead, they say that it results in a copy that won’t boot. I suspect that the customer service reps. haven’t been trained on the issue, so don’t have any more information to provide. As for WD’s model numbering system, on my PC, I found that a 360GB SATA disk that WD sent me as a replacement for a failed 160GB disk worked fine connected via USB adapter to my Windows XP PC. So, I bought four more. But, it turns out that there’s a longer model number printed on the disk (never revealed in sales literature or on the box; just printed on the disk). So, the old disk (WD3200AAJS-00YZCA0) works; one of the newer ones (WD3200AAJS-56M0A0) does not work. I assume that the newer one has 512e; the old one has just plain old 512-byte blocks.
WD has not been helpful. Seagate has some helpful documentation on the web. I think I understand WD’s product lines (e.g., Caviar Black disks are built to be more reliable than Caviar Blue); if I can figure out what Seagate does, I’m considering switching to Seagate and never buying anything from WD again.