MacOS – Boot from usb take forever

This definitely sounds like hardware issue, based on the fact that the HDD worked on a similar Macbook Pro.

Before we rule it as hardware, lets perform an Apple Hardware Test .

Apple Hardware Test (AHT) contains a suite of diagnostics that will test the hardware of your computer. It's a great way to rule out a hardware issue when troubleshooting your computer.

If your Mac was released after June 2013, use Apple Hardware Test.

Otherwise, if your Mac was released prior to June 2013, use the Apple Diagnostics Test.

Fortunately Apple does a great job with documentation, so I'll avoid repeating the instructions mentioned in the provided links.

Once the test is complete, please reply with any error codes presented.

If you have access to another mac, try this. Hold down the T key during boot on the mac with new hard drive installed. This will put that machine in target boot mode.

Connect the two Macs with either a fire wire cable or a thundbolt cable.

On the 2nd mac run the El Capitan installer. When asked where to install the OS point it at the other mac (with new hard drive installed) which should now be seen in finder. If it does not show up in finder. Launch disk utility and format the drive.

It sounds as if the USB installer is broken. However as long as you have access to another mac you do not need to make another usb installer. Just download El Capitan from the app store and follow the above instructions.