I would try first to build the compiler distribution without any patches, directly from trunk or 4.07. Then, you have the tooling in place, you can checkout your branch and try building there as well. As you noticed, you now need to add an alias in Stdlib (and your file names should be . Because the dependencies are not correct yet (the .depend files do not talk about your modules), you may need to build your module by hand, manually, by asking for make stdlib__foo.cmi in the right dependency order.
Once all the new .cmi are built, building the .cmo should work fine, and from there you can have make world working (this doesn’t build the native compiler and related tools), you can do make depend and you should be good to go.