3 flaws of genes from the perspective of a programmer
Your individual questions here are reasonable enough - although you could do a bit better at knowing some more details of the systems you are dismissing as 'flawed'. However, I think the bigger problem is your overall approach, which seems to be to make analogies between human-made computers and biological systems and then critiquing the 'missing' parts from biological systems.

Analogies like this are necessarily limited. Take the idea of DNA as 'like' a hard-drive of a computer. The nucleotides = bits, genes = contiguous segments of memory, promoters = pointers, etc. Where does this model go wrong?

Well, hard-drives are not (currently!) self-assembling structures that read themselves by coding for more, smaller fragments of hardware that additionally compress or expand parts of the structure of the hard-drive according to which part needs to be read. Moreover they don't do this while floating in liquid and self-repairing from chemical and radiation damage.

There is an excellent book called "Cats' Paws and Catapults: Mechanical Worlds of Nature and People" by Steven Vogel that covers this kind of flawed analogical reasoning between biological and human-made systems. It's not that such analogies are useless, but it is very important to recognise the limitations and fully understand why certain design choices are made by biological systems due to the particular environmental and evolutionary constraints that they work under.