If you received the server for free, you for sure can invest a bit to buy at least a decent 2 or 4 port ethernet card
Unfortunately, not every NIC chipset is supported in ROS. But this is not such a problem as many of them are already supported. Your server should accept a wide range of these cards. So, the only true solution is to replace the cards. They are not so expensive at all.
Regarding USB boot, my answer is YES, i booted every server with zero problems from USB flash disk. Actually, this is the way I boot these servers as the integrated HDD controller is not recognized by MikroTik. I use the internal USB port which can be found if you remove the lid, as the USB flash is well protected this way. Be aware that not every USB flash is suitable for MikroTik installation! I had numerous problems with them, though each was working perfectly as USB disk in any other OS (windows, linux, does not matter). I guess the problem is simple - not all USB flash disks are manufactured with equal quality! Some of them are OK, some of them are not.