In OS Yosemite the search function in Mail, Finder, Spotlight- does not work

Question

MacBook Pro (Retina, 15-inch, Late 2013)
2,6 GHz Intel Core i7
16 GB 1600 MHz DDR3
NVIDIA GeForce GT 750M 2048 MB
OS Yosemite,
Finder versión 10.10.1
Mail Versión 8.1 (1993)
In OS Yosemite the search function in Mail, Finder, Spotlight… does not work. Messages or documents with the search criteria are there and one could find them manually, but the search function fails to find them. Following advice from Apple Support (728965377):
1. I applied an Apple protocol for adware removal (Remove unwanted adware that displays pop-up ads and graphics on your Mac); I had none, because I had formally utilized a similar protocol that I had found in Internet, actually an app that implemented automatically Apple's adware removal protocol.
2. I rebuild the post boxes in Mail (Mail (Yosemite): Reconstruir buzones); It took a while but it functioned properly
3. I re-install the System (OS X Yosemite: Reinstalar OS X); It took about 4 hours but there was no problem whatsoever with the installation.
Afterwards I searched for messages in Mail, and documents in Finder and Spotlight, without any difficulty. The search function in all of them was working properly. But the next time that I needed to search messages or documents, an hour later or so, the problem reappear and a couple of new issues occurred:
1. in app RagTime 6.5.2 (Build 1821), www.ragtime.de, the menu bar disappears (it is invisible), when one performs certain operations, e. g., calculating a value with a formula, whether it is in a spreadsheet or some other component (text, drawing, etc.). After touching with the cursor the menu bar is visible again.
2. after reading an e-mail in Mail or copying an address, this is seeing as a floating object in the finder and over every application. There is no logical way to get rid of the floating object and neither copying or deleting or cutting it. It is not a big issue but nonetheless bothersome.
3. In Mail, messages with Flag or in VIP contacts cannot be seen in the appropriate folders, only in the Incoming mail folder, together with other messages. It seems to me, this issue is part of same search function problem.
4. The preview function within Mail does not show the attached documents to a message, whether it is in the IN, OUT or Draft boxes.

Answer 1

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 and start typing the name.
The title of the Console window should be All Messages. If it isn't, select
          SYSTEM LOG QUERIES ▹ All Messages
from the log list on the left. If you don't see that list, select
          View ▹ Show Log List
from the menu bar at the top of the screen.
Click the Clear Display icon in the toolbar. Then try again to re-index Spotlight. Select any messages that appear in the Console window. Copy them to the Clipboard by pressing the key combination command-C. Paste into a reply to this message by pressing command-V.
The log contains a vast amount of information, almost all of which is irrelevant to solving any particular problem. When posting a log extract, be selective. A few dozen lines are almost always more than enough.
Please don't indiscriminately dump thousands of lines from the log into this discussion.
Please don't post screenshots of log messages—post the text.
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