Assuming your fuel hose is routed correctly…..(see my signature line)
Lights flickering? Yea, sounds electrical to me…..
Check your red plug, I’ll bet you a jelly donut it’s melted.
https://fjowners.com/index.php?topic=19557.0Then..
I had a similar problem, I traced it back to a dodgy run/stop rocker switch on the right handlebar.
The 12v power to the ignition box runs from the battery through the fuse box and then thru this switch then down to the ignition box. I bypassed this run/stop switch by running a temporary jumper wire from the + lead of my battery directly to the ignition box…..and the problem went away….so I knew where to look.
Electrical woes can be maddening, so just take your time, step by step.
I’ll bet you another jelly donut that your coils are fine and that your problem resides in a switch or faulty connector.
The FJ coils, stainless steel core plug wires and resistor caps are very robust.
Melloncollie has a good point…..find out which cylinders are misbehaving. I have an IR temp gauge I take readings on the header tubes….find out which are cold and who’s hot. Prior to that fancy tool, I used a squirt bottle to see which header tube sizzled and which didn’t.
The FJ firing order is 1-2-4-3 and uses a wasted spark, so if you have a bad coil it’s going to affect both cylinders 1-4 the same (via left coil) or if the problem is with the right coil (as you sit on the bike) it will affect cylinders 2-3 the same.
Hang in there. Pat