Slow boot up on 2012 Mac mini with DIY fusion drive

Question

Hello everyone, I bought a Mac mini (2012) 2 months ago with a stock 500GB HDD.
I added another SSD to make a DIY fusion drive, and everything is working fine, except that I'm experiencing a very slow boot up.
I have confirmed both by information from the OS and some tests with command line tools, that the fusion drive itself is a success and absolutely working fine.
The slow boot up happens on cold boot only (a reboot does not have such problem).
Symptom: the Mac mini is stuck on the gray blank screen for about 40 seconds, and then finally shows up the apple logo.
Everything after this is pretty fast and fine.
I have tried the following methods and none of them seems to help:
1. Go Preferences -> Startup Disk, select the Machintosh HD. (Suggested by Apple in the Fusion Drive FAQ)
2. Verify the whole disk along with the partition with Disk Utility.
3. Reset NVRAM by holding Command+Option+P+R during boot up.
4. Reset SCM/PMU.
Does anyone have an idea on the cause of my problem?
Best regards and thank you.

Answer 1

If you have more than one user account, these instructions must be carried out as an administrator.
Launch the Console application in any of the following ways:
☞ Enter the first few letters of its name into a Spotlight search. Select it in the results (it should be at the top.)
☞ In the Finder, select Go ▹ Utilities from the menu bar, or press the key combination shift-command-U. The application is in the folder that opens.
☞ Open LaunchPad. Click Utilities, then Console in the icon grid.
Step 1
Make sure the title of the Console window is All Messages. If it isn't, select All Messages from the SYSTEM LOG QUERIES menu on the left. If you don't see that menu, select
View ▹ Show Log List
from the menu bar.
Enter "BOOT_TIME" (without the quotes) in the search box. Note the timestamps of those log messages, which refer to the times when the system was booted. Now clear the search box and scroll back in the log to the last boot time when you had the problem. Select the messages logged after the boot, during the time something abnormal was happening. Copy them to the Clipboard (command-C). Paste into a reply to this message (command-V).
For example, if the problem is a slow startup taking three minutes, post the messages timestamped within three minutes after the boot time, not before. Please include the BOOT_TIME message at the beginning of the log extract.
If there are runs of repeated messages, post only one example of each. Don’t post many repetitions of the same message.
When posting a log extract, be selective. In most cases, a few dozen lines are more than enough.
Please do not indiscriminately dump thousands of lines from the log into this discussion.
Important: Some private information, such as your name, may appear in the log. Anonymize before posting.
Step 2
Still in Console, look under System Diagnostic Reports for crash or panic logs, and post the entire contents of the most recent one, if any. In the interest of privacy, I suggest you edit out the “Anonymous UUID,” a long string of letters, numbers, and dashes in the header of the report, if present (it may not be.) Please don’t post shutdownStall, spin, or hang logs — they're very long and not helpful.