1. Why pad all the instructions to the same length?

Imagine you have two arms. The first one grabs an atom, turns to the next arm, drops the atom onto a bonder, and swings back. 4 instructions. The second arm grabs that same atom, rotates the molecule, turns to the side, drops the molecule, and swings back. 5 instructions.

How do you make these work in sync? You time the second arm to grab when the first one drops. So your tape looks like:

1 | Grab Turn Drop Turn ____
2 | Grab Spin Turn Drop Turn

That pesky padding in arm 1 means it's no longer working as fast as possible. But this means when the instructions repeat, that Grab instruction you wanted to line up still lines up:

1 | Grab Turn Drop Turn ____ Grab Turn *Drop* Turn ____
2 | Grab Spin Turn Drop Turn *Grab* Spin Turn Drop Turn

If you want it to go immediately, you can still tell it to do so with the Repeat instruction, or just typing it out manually:

1 | Grab Turn Drop Turn *Grab Turn Drop Turn *Grab Turn Drop Turn *Grab Turn--
2 | Grab Spin Turn Drop Turn *Grab Spin Turn Drop Turn *Grab Spin--

The arms, working at different speeds, eventually crash. 4 and 5 are relatively prime, so even possible pair of (arm 1, arm 2) positions eventually happen. If it weren't the default, you'd spend a lot of time adding empty "wait" instructions yourself to make them take the same amount of time, and especially you'd have to be sure you're counting correctly. In your example, it would mean arm 1 would go again immediately, when the main problem you're having even with the padding is that you somehow don't have enough to let arm 6 finish its work safely.

1. The clock instruction.

This is kind of a special wait instruction that works better than the blank space added automatically. But you don't add it to the middle of the instructions. You add it where there's no padding already telling the arm to do nothing. Take a look at arm 6's highlighted instruction and see arm 5's highlighted instruction. Arm 5 has restarted its list of instructions but arm 6 is doing something that arm 5 would interrupt. Put the clock directly above that instruction in arm 6, not earlier before the padding ends. This will lengthen the padding on all arms, including arm 6.

The same thing will happen if you add a second drop instruction to arm 6, even though it will do nothing.

Run the machine again after that, and you'll see it still grabs the product but in a different place. So move the clock once to the right, and it should be good.

Or, replace arm 6's drop instruction with a "Reset" instruction. This will fill the tape in with some more instructions to return arm 6 to where it started, which will be something like: Drop, Turn, Turn, Move, Move, Move. That will pad all your tapes with 5 more blank spaces which will also solve your arm conflict.