BigDaddy23

From the details you've given, it's definitely a corrupted HDD or a dying HDD. As the SSD is the boot drive and the HDD is not. So, this should not slow down either the SSD or the boot time. My advice to get back your boot time and still use the HDD is to go to the bios setup during booting and go to the boot option and remove the HDD from booting preferences. This disables searching for the HDD for boot files and makes your SSD the first priority. This might solve your Boot time problem. For the stuttering, I advice you to clean up your HDD by using some software and check for HDD failure and try repairing it. Or just buy a new HDD from BestBuy. I'll give the links for some HDDs. 
 
Link for some HDD models: https://www.bestbuy.com/site/seagate-barracuda-2tb-internal-sata-hard-drive-for-desktops/6344172.p?skuId=6344172
 

Weird noise could be a sign of potential drive failure, also Windows trying to fix the drive means potentially corrupt files. As long as OS files are not tied written to your HDD it would not slow down the SSD and boot time. But based on the info provided I would highly recommend backing up your HDD and running CrystalDiskMark (free software) to asses your disk health, it sounds like you might have a dying hard drive on your hands.

I hear ya! I'm my household's sole earner, a homeowner, and a dad of 3. I'm a bargain hunter for sure  

Some people here will answer you that "you must made clean install". Mostly because they knows this method only or just repeats the same statement.
 
My experience (dozens of computers) said something very different. You can just boot, wait for drivers update / change, and you'll be fine and your system will be as stable and fast as newly installed.
 
You can even remove old ghost devices using Ghostbuster tool if you really like to be more "clean" (but be careful - not all ghosted devices you should remove).
 
Different thing is your Windows license. If it was Windows with Laptop, then (like license said) you cannot move it, because you bought it as part of Laptop. System will work of course, but will not be activated. Probably. You must try.
 
BTW. Trying is much faster than asking. Just boot and you'll get most of answers without askiing.
 
 

The AF just refers to the actual product number. It's just called a Ryzen 5 1600, but it is a 12nm version. 
And to clarify that... It's a 1600AF, which is basically a 2600, not a 3600. That's because it's a 2600 with some reused memory controllers from 1600s. Neither is really close to a 3600 in power lol.
 
That aside, @BigDaddy23 your part choices are well researched, and on that 1080p monitor, they will do well  
I'm a touch concerned with a case/PSU combo. Generally you don't want those PSU units... I've seen the phillipines market, and I know both Corsair and BeQuiet! units are available out there at a decent price. I'd grab a CX 550 or a System Power 9 500W

Eh, just focus on setting everything up and playing around with it first. You can always overclock it at a later time, if you wish.

Alright, weekend stuck up with my kid and away from keyboard usually. The vendor replied me that the cheap 600w PSU and the mATX case that I choose for has out of stock, I ended up with Cooler Master MWE 80+ 500W with RM 185(USD 43). Hopefully all my parts will arrive by this Wednesday which currently the MCO had exhausted the shipping companies. My next question is, should I minor overclock it(CPU + GPU)? I had no experience on it at all, building PC I have no problem.

Those wattage-quotes are typically a little exaggerated just to make sure people don't buy underrated PSUs. 450W will do just fine.

I'm in doubt about that, one old thread stated it isn't too bad but... I'd rather go with a name brand like a corsair cxm 450w which is plenty
Otherwise you have a good build

There will be nothing wrong with the stream-quality, since the OP can just use NVENC to do the encoding.

Your planned build looks solid enough. Just make sure you get the Ryzen 5 2600AF, not the non-AF -- the AF-part is literally a slightly lower-clocked R5 3600.