when re instaling clean windows 10 is it better to remove all hard drives and leave only the ssd i want to instal windows 10

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I always do.

As said, it can be done either way but there are a few things that can go wonky with all drives installed.

Here's my guideline (may want to PRINT THIS):

0. run BENCHMARK if desired like 3DMark2001 (should get similar results after W10 install)
http://www.futuremark.com/benchmarks/legacy

Update: if games are MODDED note my note near end

1. Don't change any BIOS settings (to ensure UEFI doesn't change to Legacy if that's an option)
2. run MEMTEST (validate system memory to avoid any corruption)
3. write down e-mail and password to be used for W10 install
4. copy down applications to be reinstalled, copy any other data to secondary drive (FYI, a lot of game saves are in the Documents or Documents->My Games paths)

5...
I always do.

As said, it can be done either way but there are a few things that can go wonky with all drives installed.

Here's my guideline (may want to PRINT THIS):

0. run BENCHMARK if desired like 3DMark2001 (should get similar results after W10 install)
http://www.futuremark.com/benchmarks/legacy

Update: if games are MODDED note my note near end

1. Don't change any BIOS settings (to ensure UEFI doesn't change to Legacy if that's an option)
2. run MEMTEST (validate system memory to avoid any corruption)
3. write down e-mail and password to be used for W10 install
4. copy down applications to be reinstalled, copy any other data to secondary drive (FYI, a lot of game saves are in the Documents or Documents->My Games paths)

5. Create a W10 disc unless you have one. (I did the free Upgrade, but then had to burn an ISO image. For that I used the Microsoft Media Creation tool but chose "other PC" to download the ISO image, then burn with Imgburn for DVD or Rufus for USB thumb)
6. Shut down
7. Unplug HDD/SSD data and power cables from rear
8. Boot to W10 install

9. DELETE all content from the SSD during first part of W10 install if any exists
10. finish installation
11. check MICROSOFT UPDATES and wait until it has no updates left
12. update VIDEO drivers if you need to (*I have an NVidia GTX680 and had some problems even though W10 downloaded and installed the proper NVidia drivers. I decided to manually download the latest then do a "Custom->Clean" install of the drivers (start driver install then choose that option).

13. setup FAN profile if needed (I had to use a W7 solution from my motherboard support site to control my CPU and case fans properly)
14. ANTI-VIRUS solution
15. Other programs (from list you made)
16. re-run game benchmark and compare SCORE to pre-install

17. Attach other drives (see STEAM note below if applicable)

Some programs I like:
a) Video - Klite Standard - http://www.codecguide.com/download_kl.htm

b) Music - Musicbee - http://getmusicbee.com/

c) Image viewing - Faststone - http://faststone.org/

Other - STEAM gaming->
If you have Steam games then you can avoid downloading them again. It varies depending on how they are installed but here's an example:
a) reinstall STEAM and register (on the SSD Windows drive)
b) if "Steamapps" folder is on a hard drive point to that. (Mine is at "E:\Steam"). Simply go into the Steam settings->Download-> "Steam Library Folders"

*I believe you're supposed to delete all the files EXCEPT for the Steamapps folder before pointing Steam to the main folder. It will then rebuild/register everything properly.

VERIFY LOCAL CONTENT for each game before starting.

MODDING is more complicated. I made note of all the mods I had then RESTORED a vanilla backup of Skyrim, then re-installed all the mods. If you did not make a previous backup you may need to DELETE the game and any mod folders then download the game again (make a vanilla backup this time).

Conclusion:
I hope this is useful. I probably missed a few things but it's a good guideline. I always make a backup of my USER folder (which includes Documents) then decide what I need to copy back such as game saves. Once I'm certain I no longer need the backup USER folder I delete it from my other drive.

I should also have suggested you make a backup IMAGE of your main drive using a tool like Acronis True Image (free version for WD drives, same for Seagate but it's called DiscWizard). If W10 goes sideways you can at least RESTORE the backup image.

You said CLEAN install so remember that means NOTHING should remain on the boot drive. Plan accordingly.
 
Solution
W10 note:
I still get occasional CRASHING but my clean install worked a lot better than my UPGRADE from W8.1. Everybody's system will vary, however Microsoft is still doing a lot of work to improve things. A major update is in November but regular fixes are coming constantly.

I did visit Microsoft once. There are coders there who have a screen with color-coded bugs to be sorted. These lists change all the time but for the most part they start working on the RED (worst) codes and working their way through them constantly.
 
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