Pepper was a pun on Native Client (since NaCl = salt). Pepper Plugin API (PPAPI) was Google's more secure version of NPAPI (Netscape Plugin API). Flash Player was essentially the only thing using NPAPI/PPAPI by the end of its life.
Yes this isn't clean-room. Though none of these decompilation projects have been resolved in court yet. re3 (GTA3/Vice City decompilation) developers were sued by Take Two but they settled out of court.
All the SWFs are archived (which is often not the case on Wayback). Just when the program is requesting to load one, archive.org is returning an HTML-wrapped file instead which fails to load. It would be quite easy to add to Flashpoint.
One of the difficulties I had searching for J2ME resources is that the mobile equivalent of the JVM is called KVM (K virtual machine), so most of the search results are about Linux's Kernel-based virtual machine instead.
Don't think this was the case, what helped was it being compiled without optimizations.