The flasher indicator is wired between the hot leads from the opposing indicator lights so I'd remove that first to see if it's the problem. On my bike I used a pair of superbright LEDs wired to match the polarities to replace my indicator, one LED for each side inside the single housing.
Then, I'd check the flasher unit you've got to insure the leads match up to the socket on the bike. FWIW: I had to rewire my running light socket to match an aftermarket relay so I already know nothing's really standardized in that respect.
