You are asking for help with product photography, but the problem is that this can be one of the most technically demanding forms of photography, especially, if you want to "do it right". Because of this, good product photographers can command high payments for their services. In places like NYC, people will apprentice for a year or two under an established product photographer before they would dream to do such work for others, so don't expect to immediately produce high quality images
In your post, you brought up several issues. Let me try to address them one by one.
1. Grain / noise, lack of color detail:
I'm sorry to have to be harsh, but do you really expect to produce good quality photos from one of the earliest Nikon DSLRs. It was introduced in 2008, ie, 7 years ago. To make matter worse, you shot the main photo at ISO = 1600, so, of course you are going to see grain. In addition, you shot it using a very inexpensive, older kit lens using inappropriate settings (completely wide open at f/3.5 and 1/400th of a second), so, of course the resolution will be poor and the depth of field will be extremely thin.
If I were you, and I had no other option but to use that camera, that lens, and use ambient lighting (ie, instead of flash), I would re-shoot it at the lowest ISO on the camera (probably 100), and and f-stop around f/11. Of course, this will require a much longer exposure, but that's what tripods are for. Try it, and I guarantee you that you will see a huge improvement in the quality of your starting image. If you want even higher quality, and you can put a bit of money into the project, for a day, rent a modern camera, say, at least a d700 and a macro lens (either the Nikon 105/2.8 or the Nikon 60 mm), your images will take another step up in quality.
2. Troubling reflections:
There are well established techniques to do this, but they all rely on artificial lighting (either strobes or hot lights). You just don't have the level of control that you need with ambient light.
For an absolutely excellent introduction to this, pick up a copy of this (inexpensive) book from Amazon and read it cover to cover. It's the bible of this field:
http://www.amazon.com/dp/0240812255/
One of the very best methods to reduce specular reflections from glass in product shots is to use sheets of polarizer film over your lights, and a polarizing filter in front of your camera lens. I only had time to do a quick search for you, and found a description of this technique on the website of one the major, most widely respected mfgrs of polarizing sheet, Rosco Labs:
https://www.rosco.com/technotes/filters/technote6.html
With a bit more searching, I'm sure you will be able to find tutorials on the subject. In addition to the photography of shiny objects, the crossed polarizer technique is one of the most common methods used by on-staff museum photographers to photograph paintings (eg, for catalogs, reproductions, archiving and indexing purposes, etc.). The cost of the polarizing film for your lights is surprisingly low.
3. Fixing the above problems in post production and making the composite you requested:
There are several sayings that come to mind, but the first is
"it's useless to close the barn door after the animals have escaped", LOL. My recommendation is that before you embark on a post-production "fix", you at least re-shoot the terrarium using the settings I suggested above.
The next issue that comes to mind is that if you want to have the result look like the woods actually were in back of the terrarium, you have to realize that terrarium will act like a lens and distort the woods that you want to appear to be behind it. If you don't do this, the effect just won't be convincing. There are tutorials on doing this, but IMHO, it takes a good bit of practice to make this look believable. If you need to get something done quickly, my suggestion would be to make it an obvious composite, and not try (at least at the moment) to try for realism.
