You are criticizing gopher from the point of view of "it must have the same features as HTTP". Some of the things you call "problems" are just different ways of doing it.
And if the TCP sliding window is an issue for you, why not fix TCP?
No, these are design flaws that anything over TCP/IP needs to deal with. In particular, closing the connection to indicate the end of a file transfer is really bad (what if somebody pulls an ethernet cord?)
Fix sliding window? I don't think you understand TCP. This is an optimization to TCP to prevent the need to ACK every packet. It means fewer bytes on the wire and less CPU load for TCP processing, while also maintaining a respectable degree of reliability.
TCP checksums are not sufficient for data streams of more than a few kB.
And if the TCP sliding window is an issue for you, why not fix TCP?
Why should the server send any kind of header?
Doesn't TCP do checksums, already?