Page 85 of your owner's manual (available on Ford's website if you don't have yours) lists the rules for where you can and cannot use child restraints.
Frankly, a lot of these restrictions are puzzling to me.
• Carseats are tested with lap-only belts. Most carseats will derive very little, if any, benefit from being installed with a lap-shoulder belt.
• Is there a difference between installing in the second row center with lap-only belt and top tether, and installing in the third row center with lap-only belt and top tether? Ford provides a tether anchor for that spot in the third row, yet reading the manual makes it seem that it's not allowed to be used.
• As long as you can fit the seat and get a proper install, space between the fourth row and third row shouldn't matter for a rear facing seat. Also, the lack of top tethers doesn't matter for rear facing seats.
• Head excursion limits are identical for untethered harnessed seats and boosters, so I don't know why boosters are allowed but untethered harnessed seats are not.
The manual shows that your second row bench should have tether anchors for all three seating positions.
Let me summarize so I'm sure I've got it all straight:
Vehicle: 2006 E-350
Second row: Lap/shoulder (maybe tether), lap-only with tether, lap/shoulder (maybe tether)
Third row: Lap/shoulder no tether, lap-only with tether, lap/shoulder no tether
Fourth row: Lap/shoulder no tether, lap-only no tether, lap-only no tether, lap/shoulder no tether
Passengers:
Baby: Snugride/Marathon
2yo twins: FFing TrueFits, escape artists
Micah: Frontier85, escape artist
Jonah: Monterey/Parkway
9yo: Monterey?
13yo
15yo
16yo
Everybody needs upper torso restraint. That means either a lap-shoulder belt or a harness. Since you're not supposed to put a harnessed seat in the fourth row, that makes your fourth row a two-seat bench.
You are going to have to decide if you would rather put a harnessed seat (or two) in the fourth row, or put an older child in a lap-only belt in the fourth row.
Ideally, everyone would also have head support. There's not much you can do for adult-sized people, but it is a good idea to keep your kids in high back boosters for as long as they fit. Even if the lap/shoulder belt fits properly without the booster, the head restraint provided by the booster provides additional protection.
Here's what I suggest for arrangement:
9yo, 13yo, 15yo, and 16yo: outboard in lap-shoulder belts, third and fourth rows.
Jonah: Sounds like he's new to boostering, therefore younger and may need help with his belt from time to time, or at least a visual check. Second row in lap-shoulder belt. If he doesn't need help or checking, it doesn't really matter what row he goes in. He could swap with any of the older kids.
That leaves baby, 2yo twins, and Micah to go in the fourth row centerish, third row center, second row center and second row outboard. Would it be possible to put the baby in the fourth row, rear facing, and someone still be able to get to the seat on the other side? That would leave tether anchors available for all your forward facing kids, but I'm guessing it's not possible.