It seems to me that the best ender on a standard launch combo is (f2, 123~zod charge) for damage or (f2, 123~trait) for setups. The timing is a little tight, but it's easily learnable with a little practice.
The next thing is that, in general, the MB ground blast is the best linker for most combos, since it scales less than the MB rifle. The exception to this MIGHT be when you are linking multiple rifle shots in a single combo, since you need the higher launch and slower fall. I'm not sure about this, though, and need more lab time. It should be noted, however, that juggling your opponent BEFORE the MB ground blast changes the combo. If your opponent is launched by the MBgb, then you can get a b3 off. If they are launched before the MBgb, then you have to do a ji3.
Starters are more obvious. Without meter, you're going to get by far the most damage out of f21u2~air rifle. With meter, f21 seems most damaging, while 112 and d12 are the quickest punishers, and 213 is your safe overhead. However, I suspect b12 has some hidden properties that need more examination.
With Trait, the situation is a bit different. You either need to generate a juggle really quickly via 3 or f213, or you need to meter burn. If you get the quick juggle, then you go into the Kickball Loop. If you get the meter burn, you need to use the swipe, swipe, swipe, grab setup to bring them down to earth.
Finally, in the corner, there's no reason to really go for anything other than rifle combos. They're meterless, do high damage, and are repetitive enough that you're unlikely to drop them. Basically, you just want to get a juggle into an air slow rifle, then an air mid rifle, then an air fast rifle, into ender.
So having said all that, I THINK the most optimal combos right now are as follows (note that these are meant to provide examples of his combo structure to be extended to other combos):
Meterless:
f21u2~db1b, ji2~db1, dash, 123~bf2/4 - 38%/Wraith
1 Bar:
f21~db2 MB, dash, b3, ji3, f2, 123~bf2/4 - 44%/Wraith
f213~db2 MB, ji3, f2, 123~bf2/4 - 42%/Wraith
Trait:
f21~db2 MB, 4, 4, 4, d4, db2 (hold), B3, J3, 3~bf2 - 52%
j3, 3, 4, 3, 4, 3, 4, 3, 4, 12~bf2 - 55%
Corner:
f21u2~db1b, j2~db1, j2~db1f, f2, 123~bf2/4 - 43%/Wraith
There's one other set of combos that are really important to Zod's game, and those are his ranged combo starters--especially using his Wraith: Mr. Snuggles. If you end one of his combos with 123~4, you have a full-screen guessing game that's way in Zod's favor. From 123~4, you can do one of several options:
a. Ground laser (hold)
b. Wraith grab
c. Rifle (air or ground, MB or regular, slow mid or fast)
The latter two options are simpler and more obvious. The grab is an overhead that leads to full combo. The rifle is mostly a deterrent that keeps your opponent from charging or jumping in, forcing them to sit in your "vortex" for a while. Where the magic happens is with the ground laser.
When you hold the ground laser, your opponent has to make a quick guess and, if you have decent reactions, you can react to their choice. You can stuff ground movement by releasing the button for the explosion or meter burning the laser, or you can blow up the low block with the overhead grab from Mr. Snuggles. You can also have Snuggles smack them if they try to jump or use one of their own moves. If they have an option for fast forward movement (air or ground), you can dash (back or forward) out of the ground laser and have Snuggles grab them for combo. Another great option for additional mind games is to shoot your ground laser a bit in front of them and THEN meter burn it so it moves toward them. So having said all that, I submit that the following two combos are perhaps Zod's most important options, since they allow for ~40-45% combos from a full-screen vortex with his trait out:
d4, dash, db2 (full charge), b3, ji3, 123~bf2 - 39%
db2 MB 4, 4, d4, b3, ji3, 123~bf2 - 46%
Note that you can also do the second combo (without the ground laser) if your opponent gets hit by a rifle shot:
[rifle shot launches], 4, 4, d4, b3, ji3, 123~bf2 - 42%
So there's my attempt to start consolidating Zod's combo options!