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I use Mendeley for the general literature management, sorting, commenting and syncing. Most of the time I write in Latex though, so coupled with Bibtex for references. Mendeley can export its libraries to Bibtex, but I also have a bunch of manual Bibtex libraries (since I only started using Mendeley this year).

Basically, Latex/Bibtex is just wonderful for the bibliography part of your publication or thesis, because it is amazingly customizable and as automated as possible. You could change your mind about citation and bibliography styles every other day and it wouldn't be a problem. Insert the tag as you write and it will always link to the right publication (like most people I tag them with AuthorYear because it's the simplest way to get unique tags/identifiers).

What I love about Mendeley is that I can throw any remotely interesting article in my library, read it later, add highlights and comments, sort them into subfolders. Any relevant publication info and abstract is automatically read and added. It has automated file-naming and syncing across devices (which is lovely for working at home with all the journal articles you can access at work/uni).
One thing I often wish was more automated is the addition of the PDF files. It automatically downloads and links the file if it is a freely available article (Pubmed Central, for example), but generally doesn't if it is a paywall article that I have access to. Even if I am staring right at the opened PDF article, I have to manually download it and link it to the Mendeley entry of the article (which is created with one click on the Mendeley bookmark). Call me lazy, but I wish I could save that step, although I am not sure if that is technically possible. Maybe it's not Mendeley's fault.

I sent you a PM with the file.

Personally, I would not put a strong focus on the bachelor thesis. Mention briefly what you did, the methods you may have learned and then talk about transferable experience, like attending research group meetings and discussing your results, insights into how to approach your own project, how to acquire samples/subjects etc... there is always SOMETHING. Your audience will not be too interested in the specifics of your project if it is unrelated.
Then I'd talk about how you progressed during your master's what subjects you chose and how your interests evolved. Anything that drew you to the topic you are applying to. And then I'd talk about the planned thesis. Even if you have not started it yet, you probably have a plan what it's going to be? Talk about the background, what you expect to find, what you expect the difficulties might be. In the end, that not only introduces your research topic but also that you have foresight and planning skills.

I agree, have a look around for English programs. I would advise you against choosing a German-taught degree in your situation. Even if you take language courses and meet the formal requirements it can often be difficult to follow (even if you understand it all, it will take you longer to process it, understand, take notes,...). You will progress better in your studies with an English program.
You could then still take a German course for everyday life and to communicate better with your teachers. Almost all universities have a language-learning center that offers affordable, or sometimes free, courses for students.

Your profile looks okay. As Walter said, papers and other activities are not expected of undergrads planning to start a master's. The most important part is how well you did in your bachelor's and if it is comparable (by that I mean similar workload and amount of classes, and completed with a thesis project). The project in an automobile company will be your thesis for the undergrad degree, I assume?

An additional word about Uni vs FH. Walter already explained the difference, but do not be discouraged by the "inferior" because that is mostly an academic perception. And it does not mean that these studies are easier or have lower requirements. Generally, you could say that FH degrees are more industry-oriented. If you would like to do a PhD/do research, a university is better, but if you plan to work in the automobile industry, FH works just as well. Especially if they have connections with companies and work placements integrated in the studies.

There is an article on FindAPhD about funding with charities:

Maybe this would be a better option for you? It saves you a lot of risk, possible legal costs, anxiety. You won't burn bridges with anyone and might still get the financial support you need. You are on a good path to completing the PhD while balancing it with child care, I cannot imagine that all charities would turn you down.

That sounds indeed really stressful. And your supervisor does not seem to have realistic expectations. You just cannot collect samples faster if there are none available locally that fit your criteria!

Is there any way to prove to him that you just can't get more without external samples? I am thinking along the lines of maybe a hospital database of registered patients and how many have the characteristics you select by. I assume you do not have direct access to patient data in any case, but you could find out who handles this in your department and ask them if they could help you with an anonymised statistic. For my project, I have such a list of all the cases admitted here since a certain year which fit my criteria.
Not sure if that is applicable in your case, but something similar could help you convince your supervisor that his expectations are impossible. He either has to budge on the external sources or has to accept that your sample size will be much smaller.

Well, for English studies the UK seem obvious. But there you really need to watch out for funding because otherwise the fees are really high.
An alternative suggestion would be a Nordic country (Denmark, Sweden, Norway, Finland). They have a high quality of education and no tuition fees, and they are also very welcoming towards international students.
I know some people who went there for studies who had really positive experiences. I researched some universities myself because I considered doing a master's degree there as well. Ended up in the Netherlands instead (which is also nice, but I am not sure about the fees for non-EU students).

In your case a control could possibly be comparing a normal (non-cancerous) sample to another normal sample as a test for just regular variation within the same organ.

I feel your pain regarding the collection of samples. I have a similar (sequencing) project where I need to collect tumor+normal samples from patients meeting certain criteria, which is really slow. I will also not have as many patients as I'd want to but I'm "only" an MSc student, so for me it's okay. No pressure to publish, my project has a fixed duration and my supervisor can build on it either way.

However, because I am also not experienced enough in biostatistics, I just contacted someone from overseas who is. When researching I found a lot of papers from two researchers which were directly related to my problem, so I just sent them a friendly email explaining what I do and if they could help me. It has given me a lot of insight into what amount to data I (or my supervisor) should shoot for, and how to proceed with it.
Maybe you could find someone who could discuss your statistical issues with you too?

What are your supervisor's expectations of how you should get the samples by the way? If he does not want collaborators from elsewhere then I assume he wants to get samples from a local hospital?
Also, how did you phrase it when asking about collaboration? I mean, there is also a difference between collaboration and requesting tissue. I am also using tissues I got from other national hospitals but I am not actually collaborating with them (in that they will not have any co-authorship whatsoever once there is a publication). Maybe there was a bit of a misunderstanding and your supervisor just didn't want to share the glory?

Personally, I would wait for the interview since they already scheduled it. You can see how it goes; if you think Uni A could work out and you have a good feeling about the interview, you should mention it at the end (explain briefly what happened, why you went for Uni B and that Uni A would still be your first choice).
I do not see you as wasting their time either. As a university, of course I would make sure that the student is still interested (i.e. has no PhD position yet). But in your case you definitely are interested despite already having a position.

Sorry mate, I checked but my institution has no access to this journal. I would also suggest you ask at your university library. Alternatively, there is always the option to email the authors of the article.

Fun little survey.
I found the fancy buttons a bit buggy, and for some reason I had more than one 50th question. But now I'm really curious what will come out of your study. Good luck with the further research!