I see what your saying. The pot is wide but not as deep as would be normal in a "stand-up" stove of that size. As regards to the grates, I don't think your mods will be any problem because you were smart enough to only make a small change and not be too aggressive. The liner is another store? I see what your saying with the problems. I wonder if it wouldn't be best to try a liner using the "plastic" or clay refractive material that I used? It can be modeled just like clay with a mallet and is "sticky" enough to stay were you want it. You could do the parts inbetween the "teeth" and the unsupported top frame. It's strange that they have those holes like that? But maybe because it burns bottom to top?
I still have a half box left from the cookstove box I made for my Glenwood C. But I'll use the rest on the new stove "Cartman" because Kim says the Modern Oak 116 is allot chubbier that the Herald!
I noticed that you got the Sunnyside from Bryant's. I know they have that clay type plastic refractory material. If you want to get some and have a problem finding it, let me know and I can probably get some for you although it might be expensive to ship as it's quite heavy before it drys. Oh, and I think your are right about the back of the pot for banking.
Also I wanted to say that the nickel looks fantastic! The stove is a real "looker" and the pieces you chose to nickel were just right!