I was debating whether to put this thread in Language Learning or LOTE, so hopefully this ends up being the right one!

Anyhow, I'm only into my fifth semester of Japanese (3201 level in U.S. Universities), but thanks to me and a classmate being partners in analyzing the language, we've noticed a few patterns in the way words work in Japanese. Specifically, I've noticed a pattern in a certain class of compound verbs:
(While this specific class of compound verbs is unrelated, this can probably help to explain the formulas) Suru verbs, probably the most populated kind, are created by either taking a loan word, or making a compound word from at least two Kanji (Typically using their ON-Readings*), and tacking する ("Suru," to do/make) at the end of it.
Example, you have these two kanji:
1. 習 (ON-Rdng: "Shuu" | Meaning: Learn)
2. 得 (ON-Rdng: "Toku" | Meaning: Gain, Profit)
When both are put together, they make 習得 ("Shuutoku" | Learning, Acquisition), and when made into a suru verb, make 習得する ("Shuutoku suru" | Learn, Acquire Knowledge, To Master)
Easy as making stew, right?

Well, some of the more common verbs in Japanese are also compounds, but use a different kind of compounding method involving Kun-Readings.* All one would need to do is take the "stem"** of one verb and tack it before another verb, and voila, your new verb!
Example, you have these two verbs:
1. 思う (Kun-Rdng: "Omo-u" | Meaning: To think) Its stem is 思い ("Omo-i")
2. 出す (Kun-Rdng: "Da-su" | Meaning: To put out, take out.) Its stem is 出し ("Da-shi")
If you tack the stem of 思う before 出す, you would get 思い出す ("Omoidasu"), which means "to remember." In another case, 込む ("Ko-mu") is added after many stems to often indicate an action done completely or intensely, like with 飲み込む ("Nomikomu"), which combines the stem of 飲む ("No-mu" | To drink) with 込む ("Ko-mu" | To do completely/intensely) to mean "To Swallow".
Finally, as every Japanese-language student learns within his first few lessons, changing the final "-u" to "imasu" (on "-u" verbs) or dropping the final "-ru" and adding "masu" (on "-iru/-eru" verbs) creates the polite form of a verb. 行く("I-ku") becomes 行きます ("I-k
imasu"), 食べる ("Ta-beru") becomes 食べます ("Ta-be
masu")
Now that I'm done explaining some formulas of Japanese compounds, I can finally explain my little hypothesis XD
Upon examining the polite form, it's apparent that we have a verb in its stem form followed by "Masu." Knowing this, and using what I know of Japanese's grammar mechanics, this leads me to consider that the "masu" one adds after a verb stem could possibly be not a conjugation, but instead a verb of its own, likely with a meaning akin to doing something in a respectful or polite fashion.
Of course, I am also aware that to normally make verbs negative or past-negative, the final "-u" must be changed to "a" and "nai" or "nakatta" added after. But, looking at the negative and past-negative forms of polite Japanese verbs (ません["masen"] and ませんでした ["masendeshita"] ), something seems to contradict my statement. This presents (so far) three ways I can view this:
1. As a verb, "Masu" would have a negative and past-negative conjugation of "Masanai" and "Masanakatta," except that isn't the case. Because "Masen" and "Masendeshita" aren't consistent with this, "Masu" might not be a verb at all, but simply a polite conjugation method as it is taught to be.
2. If "Masu" is a verb, it's likely an irregular verb like Suru, Kuru and Aru, which would explain the non-standard negative endings.
3. There could possibly be a type of grammatical conjugation that explains this later on in my studies, and I just simply need more information. I'm taking this stance for now.
Have any of the Japanese speakers/learners given thought to this? Would anyone have clues, maybe answers?

Footnotes:
*Most Japanese Kanji (The more complex characters), because of their Chinese origin, have multiple ways of being read, and from those readings derive different meanings/words. ON-Readings have their roots in Chinese language (年 has an ON-reading of "Nen" is Japanese, and is read "Nián" in Chinese), while Kun-Readings are a native Japanese word (所 has an ON of "Sho," which is part of the word 場所 ["Basho"], but has a Kun of "Tokoro," which is expressed when writing the Kanji 所 by itself.)
**To make a verb stem, for "-u verbs" one must take a verb's plain form and change it's final "u" to "i." (行く ["iku"] becomes 行き ["iki"] ), and for certain "-iru/-eru verbs" one simply drops the final "-ru" (食べる ["ta-beru-"] becomes 食べ ["ta-be"] ) Sometimes the stem is used by itself for an infinitive.