Checking the switch matrix chart, it looks like those 3 are all on the same row--row 4. Are you sure all 5 of the loop buttons are working? One of them, referred to as Loop 4 on the chart, may also not be working. Also, check that wiring and diode are firmly connected on coin chute 3.
Whatever the case, each of the 5 switches listed on the chart for "Line 4" will have a violet wire with a black stripe. That violet-black wire daisy-chains from coin chute 3 switch to the P lane switch, upper left pop bumper switch, loop 4 button switch (on the u-turn), and the S lane switch, and ultimately from the one of those switches on the playfield up to the MPU at connector J5, pin 14 and/or J6 at pin 8. So you should have continuity on that wire (violet/black) between all those switches and the violet-black wire at connector J5 and/or J6 at the mpu. All it takes is a broken wire or diode on one of those switches to take out the whole row.
Also, have you re-pinned the connectors between the playfield and backbox? These games are notorious for bad connectors in that region.