so enable the required hse flags/settings for sample blinky program and test?
Yes!
From the various threads here (and on the ST forum) it's quite clear that there are multiple things going on. First it was the question about the external clock, which you claim to have solved. Then it was the issue of the internal bootloader starting up, even though you don't want it to. This is strange, as you wouldn't be able to switch to an external clock unless your chip runs your code (the internal bootloader runs from the internal oscillator). As Pauli said, the (rhetorical) question is, how did you verify that you indeed ran from the external oscillator, after you fixed it? You know there is a bit in on of the registers that tells you if the HSE is ready, right? Right???
Lastly, there is the issue of the nondescript binary that you're trying to get to run for some VCP (virtual Com port, I assume) function via USB. There are multiple potential failure points here that would all need to be checked (again, as Pauli said). It sounds like that was running at some point in time. So, can you go back to that original hard- and software configuration to make it work again?
So, yes, the best course of action is to check one thing at a time with as simple as possible code, then incorporate that code into more complex code. USB is not simple.