Swap the lines on the fuel distro, ie, put # 7 fuel line to # 8 hole on distro. If misfire follows the "hole" they you know it's the distro
If ignition parts have never been done I feel as though your indy is kinda wasting your $$..it's time to freshen those up. Plugs are worn by about 15-20K, cap and rotor is spent by 50-60K @ best!
Jonathan