Electrical – Convert 4 gang to 3 gang switch box

Don't pay attention to the colors

The red wire going to the existing switches in your box is actually a pigtail from the hot feed coming in (the junction of the two blacks), while the two black wires from the switches are the switched feeds going back out.

So, nut the black hot wire from the timer to the existing junction of always-hots that you've pulled out and a pigtail to provide always-hot to the other switch, while the appropriate black switched wire gets nutted to the red wire from the timer. The timer neutral goes to the neutral junction (white wires) that you've pulled out, and the timer ground goes in with the rest of the grounds (which need an actual wirenut on them FYI). Finally, the yellow 3-way wire can stay nutted/tape-insulated off as you don't need it, as you have already indicated.

You have 3 dimmer switches, so if you want to keep them (or combine all the recessed lights into one) you won't want to use any combo switches. Based on what I can see with the wiring, you could attach all the lights to one dimmer (check the wattage rating on the dimmer, but you're going to replace the recessed lights with LEDs anyway, right?). That would leave one dimmer and one regular switch and those would both fit into a single 2-gang box.

If you want to minimize the amount of patch work you do, you can just replace the two boxes with a 4-gang, but you't going to have some repair on the edges either way. I hate having to do drywall repair, so I personally would try to make a 4-gang fit as best as I could, but that's really just preference. I can't think of a reason they used two boxes other than that's what they happened to have on hand at the time.

When you do replace the boxes, make sure the new box has the proper wire clamps on it. Right now I bet the wires are just fed into those boxes with no clamps or anything to cover the sharp edges of the knock outs. Look for damaged insulation on all the wires.