the missing link between species counterpoint and actual writing

hello everyone, this is my first post, I am glad to have found this place!

I am doing my species counterpoint believing that there would be few instances of broken rules in actual works. I thought that I would have to be very strict when writing a countersubject for example. Below are the beginning lines from invention 1 and fugue in c minor on which I have marked intervals that are "forbidden". How can I make the jump from strict species to actual writing?

thank you in advance,

Aristides.

In the first case I would do this:

In the second I would rise the C to a D (in the left hand)

thank you for your kind reply.

I realise these particular problems could be solved, but these are famous Bach tunes. I am wondering how to move from the species rules of counterpoint to actual writing of music. It seems that whenever I look at proper musical pieces, fugues etc, even the Fux book, the materlial is full of non-adherence to the rules. Is there a book, course, or something that can help me bridge the gap from species counterpoint to composition?

(personally, I like the C-F# tritone in the example, it is the defining tritone of D7, but I understand it is not to be used under strict counterpoint...)

First. you have to realize that the rules of species counterpoint can be altered (or simply abandoned) to enable the function of harmony and harmonic structures. Second, the Bach examples are great examples of passing tones. When you listen to these passages... you can clearly hear that they are passing tones meant to ornament the line. So, what you've found here are examples of Bach altering the rules to fit the harmonic structure underpinning these passages. Third, there are different types of 4th intervals: diminished, perfect, and augmented. Not all of these intervals were considered untouchable. 

Finally, while it is awesome to devote time to species counterpoint and the Fux method, I'd advise not sweating the lack of application in the repertoire. The purpose of studying species counterpoint is to learn how to start writing for multiple voices. Fux method is great for getting one familiar with part writing -in particular, how to make each line sound independent within the overall sonic landscape. Outside of this, once you have established basic part writing mastery... then you're free to manipulate and abandon that method all together.

thank you for the reply. the accented passing notes (not to be found in species) were a revelation to me!