Small update: I tried extracting the Valve crosshairs again using gfscape and overwriting crosshair5_valve.vtf, this didn't work.
I then tried changing the rifle's script file to read
"crosshair"
{
"file" "vgui/replay/thumbnails/quarteredcircle"
"x" "0"
"y" "0"
"width" "64"
"height" "64"
}
This did successfully change it to the quartered circle that came from cfg.tf.
I also tried removing my custom hud (m0rehud) and a couple of .vpk's I wasn't really using and found that it didn't make a difference. I'm using mastercomfig low + customizations so I tried adding the transparent viewmodels addon and that hasn't made a difference either. Very bizarre but I'm not sure what else to do so I'll just use my sniper script to set crosshair 5 ingame for that class only. Thanks again for the help