Why is my bran new 2TB ssd taking 3-5 minutes to boot win 10?

The first things I would check is to make sure the wire connections are secure and check how how it's getting while it's running. It's going to heat up and get pretty warm but it shouldn't ever be getting so hot that you can't rest your hand on it. If it's getting that hot that you can barely touch it you may need to relocate it in the case and put it near a fan, or make sure there's open space all around it so it's getting air flow to try and keep it cooler. It might get a little warm even just from windows booting up. It shouldn't be getting too hot to touch. Digital memory acts up when it gets too hot, same kind of thing with when a cell phone or tablet gets too hot it starts running like crap.  

Did you create partitions on it or did you just throw it in and install windows on the entire 2TB? If you didn't create partitions and left the drive be the whole 2TB of space that right there might be the problem. Windows is looking through all of that space for indexing purposes (it gathers everything on the drive so it can be found quickly when you open file explorer, and for the times you search for a file by part of it's name) when it boots. It there's a lot on the drive, or just a crap ton of space it has to go through, that can effect boot times.

There are tons of good reasons to put the operating system on its own, small, partition and that's one of them. If you didn't partition it it might be a good idea to do that before you start installing all your programs and stuff.

Microsoft claims win10 requires 16gb free space for it's installation and to run. 

There are some programs that just don't run right if they're not installed on the primary drive with windows so it's best to leave room for them. It's a good idea to make the primary partition (the partition with the operating system on it) 200 to 250GB and make other partitions on it the same size or in multiples. I generally make storage partitions 500gb. 

Even if you use the ssd as storage only, which is an option to put win10 on one of the other hard drives and partition the ssd for storage only, you should still create different partitions not just one gigantic one. Thank God solid state drives don't need to be defragmented. Defragmenting 2TB of space would take forever. 

Another thing it could be is your anti-virus scanning before it allows windows to launch. Some AV's, like Krapspersky, do have options you can enable to do that that might be enabled by default when you first install it. Check your AV to see what it's doing during startup. You do want windows to start your AV when it boots but you don't want your AV scanning anything right away. 

Normally a slow boot up is caused by either too many programs in the boot menu or one or two programs that have terribly slow boot routines. Give the following a shot. it'll teach you how to stop things from running during boot up. <<<<< Slow Computer – Disable Startup Items

Generally if a computer "used to perform well" and now it doesn't I always suspect what is starting up and what may be running in the background. Most software during the install process will set itself up to start at boot up with everything else. The goal would be to have as little starting up as possible. Basically all that I normally recommend is to have Windows, antivirus, and possibly an anti-malware program booting up. You really don't need other programs consuming your resources if you are not currently running them. So here's a simple way to disable a lot of unnecessary programs from running. Go to an open area on the Task Bar and right click once. In the list that appears left click on Task Manager. A small window will open. In the row of tabs at the top of the window lift click on Startup. This displays a list of the programs that are booting up and running in the background. Too many things running simple consume your ram and some CPU resources. Look over your list and decide what you don't need to run all the time. For example, if you are a Chrome user there is no need to have it running all of the time unless you are currently browsing the web. To stop it simply left click on it once to hi-light it, and then go down to the lower right hand corner of the window and left click on "Disable". You'll see the word "disable" in the third column so you'll know its status. Now go through the entire list and disable as many unnecessary programs as you feel comfortable with. You can always go back later and "Enable" any program if you so desire. Once you've disabled as many as you can, simply Close the window, and then reboot your computer. Go back to the list and double check it to ensure it's as you want it. You should see some improvement in your computer's performance. >>>>> Good luck and I hope this helps.

I've had situations where bad secondary drives will cause slow booting or even no booting on an SSD. Unplug your old drive and see if it boots properly.

Some possibilities: 

1. It's just a caching issue. Over time, Windows should set up a prefetch cache so that boot times are quicker.

2. Your partitions are misaligned. For optimum performance, partitions on an SSD should be aligned to a sector barrier, usually a multiple of 4096. The Windows 10 installer should align the partitions correctly automatically, but if you manually set up the partition, there could be an issue.

https://www.thomas-krenn.com/en/wiki/Partition_Ali...

3. There's a bug in your SSD's firmware. Install the Western Digital SSD dashboard and see if there's a firmware update.

https://support.wdc.com/downloads.aspx?p=279

4. You don't have the proper chipset drivers installed or they need updated.

5. Your drive is defective in some way, such as defective cache. I'm not sure what the best way to test for that would be

6. Your drive is counterfeit.