1. The Shema when a Jew wakes up is normally part of Shacharis. As for before bed, I don’t really have any tips because this isn’t something I ever struggled with since I got into the habit of spending some time talking to Hashem informally before I went to sleep a good 5-6 years before I started becoming more observant, so adding Shema to that was not difficult to remember. Perhaps putting a sign by the bed as a reminder or something.
2. Depends on the situation. When I started saying brachos I was living in a dorm and all my food came from the dining hall, which I had to swipe into with my ID. So I put a sticky note on my ID that said “bracha.” That usually worked and then I eventually just got in the habit. But for someone who has their own eating area in their living space obviously that’s not going to work. It might help in such a situation to try to slow down while eating and do so mindfully, remembering that the purpose of eating is to strengthen the body to serve Hashem, and that Hashem gives us food, so we should thank Him for it.
3. Are you more afraid of human beings than Hashem? Not saying a bracha over food is equivalent to stealing from Hashem. It’s not too difficult to say a bracha in a subtle way. As for the larger issue, it’s a bit difficult for a Jew to hide their Jewishness and not work on Shabbos or the chagim at the same time. Antisemitism is something that, unfortunately, all Jews do face at some point, and I would’ve hoped the people involved in your Jewish learning would have strongly emphasized that reality when you expressed your interest in Judaism. Many, many Jews not so long ago would go home every Friday afternoon knowing they would be out of a job on Sunday because of not showing up for work on Saturday. You don’t even know for sure that there would be a problem if people at your job knew you were Jewish; they knew again and again for sure that there would be, and nevertheless continued keeping Torah and mitzvos. Hashem rules the world, not antisemites.