Each kana has one and only one associated sound. Their sole purpose is to represent sound.
Each kanji has one or more associated meanings and one or more associated readings.
As you know by now, the set of kana is limited to just exactly the number necessary to transcribe the sounds of the Japanese language. There aren't a whole lot of them. As you have also noticed, the number of kanji is staggering. People can argue about the actual number of kanji or about the number you need in order to get by, but in either case it is abundantly clear that the number of kanji far outstrips the number of kana.....a pretty good clue that simple one-to-one interchangeability is likely not a feature of the blended writing systems.
Kanji were borrowed from Chinese, a language which other than being an Asian language really has nothing in common with Japanese, meaning that jamming the Chinese writing system onto the Japanese language was guaranteed to be a square-peg-into-round-hole proposition.
Different kanji were borrowed from different areas of China (with different dialects) at different times. In cases where there were already native Japanese words to express a concept, all that was needed was a symbol to represent the meaning....the symbol could be read as the native Japanese word (kunyomi). In other cases, it was necessary to also borrow the Chinese reading (onyomi) of the kanji. The sounds of Chinese and Japanese are very different, so the borrowed sounds got modified to fit the sounds of Japanese. Chinese readings are also commonly (though not always) used in the case of words compounded of two or more kanji, including cases where one or more of the kanji when alone may represent a native Japanese word and thus have a native Japanese reading, they also have borrowed Chinese readings for use in compounds. Which reading gets used for any kanji or group of kanji depends entirely on the context in which it is used. (In the study of Japanese you will hear the word "context" until it makes you want to jab icepicks into your ears. The answer to everything about Japanese seems to revolve around context).
Let's take a look at one of my favorite examples, always a sure bet to dispirit anyone contemplating learning to read Japanese:
東
東海
東海運
The first kanji means "East" and is (usually) read ひがし. In the second line, we have added the kanji meaning "Ocean" and usually read as うみ. So that should be ひがしうみ, right? No....it is とうかい. In this combination, we use the onyomi (Chinese readings). Now, I'll tell you that the third kanji in the last line means "transport" and the onyomi is うん. So that should be とうかいうん, or perhaps the beginning reader might mistake it for ひがしうみうん. The actual reading is あづまかいうん and it is a company name. Taken in isolation, there isn't a Japanese person alive who can tell you with complete ontological certitude whether 東 (with no contextual clues) should be read ひがし or あづま. It is an impossible task. Same goes for 大和. Nobody can tell you whether it is だいわ or やまと. Is 八幡 read やはた or is it read はちまん? Same deal....seeing only 大和 or 八幡 in isolation, it is impossible to say for sure.
So back to your question about 行 and い:
If you recall, I earlier mentioned that Japanese verbs have their inflected portions represented by kana, so you can tell what tense the verb is. The portion which conveys the meaning of the verb can be represented by kanji. The concept of "to eat" can be represented visually by 食 and even if you haven't the slightest idea how to read it, you can be damned sure it has something to do with eating. The verb "to eat" in Japanese can be expressed as たべる (among other things, but let's keep it simple for now). We can use kanji to write it as 食べる. That doesn't mean we can read that kanji as た anywhere we see it. For example, 食事 is read しょくじ. So is しょく always associated with the idea of eating? Nope. 職業 is read しょくぎょう and has nothing to do with eating. 十色 is read じゅうしょく and the しょく portion has to do with "color". This is just a roundabout depressing way of making the point that there is no one-to-one correspondence between the sounds of Japanese and the system of representing meanings with kanji. It is a mixed up, messed up, muddled, absolutely impenetrable tangled terror....which actually isn't all that bad once you get used to it. Unfortunately, the majority of foreign learners give up before they start to get a grip on it.
If you have a sentence containing 行きます you may change the 行 for い if you wish. After all, the word is read いきます. All you will have done is to change from a meaning-based symbol to a sound-based symbol. On the other hand, if you see something like だいすき you may not remove the い and replace it with 行, changing it into だ行すき. Nobody would even guess that you meant it is だいすき and would probably read it as だぎょうすき, which is gibberish. Even though it for all the world looks like a totally screwed up writing system, there is method to the madness and you can't just throw things around willy-nilly. You and I share the misfortune of having had to approach this task with the very very large disadvantage of not already knowing the language, which makes attempting to learn to read Japanese text doubly difficult. Native speakers catch a major break on that count.
To further confuse the matter, sometimes 行きます is read ゆきます. With different okurigana it is 行います and read おこないます, with a completely different meaning. Back to our in-isolation-nobody-can-tell examples, if presented with 行っている without context, nobody can tell you for certain if it is いっている or おこなっている. Of course, we can also see that kanji in things like 銀行 （ぎんこう), where it has the reading こう. Or in things like 行列 (ぎょうれつ), where it has the reading ぎょう. You might be tempted to look at those last two and surmise that when in the final position it is read こう, but that would be a mistake. In something like 東京行 it is read とうきょうゆき (Tokyo-bound), sometimes written with き on the end and sometimes without. Ain't Japanese fun! (And do you start to see what I meant when I mentioned earlier that if the prospect of learning the kana seems a daunting task then it might be wise to consider whether learning Japanese is a task you wish to tackle or not? I wasn't being an a-hole; I was merely giving fair warning of what lay ahead).