Steven,
The `bond` command is available in the ChimeraX daily build. They've also added this capability to the 'Build Structure' tool in the daily build.
I can't speak to why you're getting an error in Chimera - maybe Chimera is still interpreting the input as two separate models? Based on your example command, one of the molecules (#0.1) is a child of the other (#0), which would technically be a separate model. I don't work with PDB files too often, but look out for MODEL/ENDMDL in your file. If those are present, they'll define separate models.
If you're bent on doing this in ChimeraX 1.1, my SEQCROW bundle has a bond editor tool (Tools -> Structure Editing -> Bond Editor). You just select the atoms you want bonded and click 'draw bonds between selected atoms'. With the bond command imminent, I didn't bother adding my own command. It just made sense to have that capability on that tool. The atoms will still need to be on the same model.
Depending on how much you're adding, you might also be able to use SEQCROW to attach monosaccharides to residues or each other as 'substituents'. SEQCROW cannot put an added substituent in its own residue (yet). I can imagine this limitation might make using SEQCROW for this pretty awkward. You'll also have to add your saccharides to the list of substituents SEQCROW knows about. The process for this would look something like:
1. open/build a saccharide
2. open Tools -> AaronTools -> Add to Personal Library
3. select everything except the OH of whatever is going to be linked to another residue
4. enter a name on the tool
* ignore conformer stuff, it's only used by a different program
5. click 'add current selection to library'
To add this substituent to a SER residue, for example:
1. select the SER's H on the hydroxyl group
2. add the saccharide using the command:
* run `substitute sel substituent