Regarding the general architecture, mind that a considerable amount of modules predate the PDP-1.
Before the PDP-1, DEC was exclusively in the business of designing digital modules for lab purposes and the PDP-1 was meant to be constructed from those. It didn't just work out like that and the PDP-1 incorporated also custom designed modules, but this is also how it was possible to design the computer in just three and a half months.
Regarding timing, I think most existing emulators will get the timing right at memory cycle granularity (5 µs). Which is what mostly matters externally. The notable exception here is the automatic hardware multiply/divide, which inserts a timing chain of its own and will complete in variable time. (MUL will complete in about 14-25 µs and DIV in about 30-40 µs. Usually, emulators will use the respective average, which roughly coincides with the average execution time stated by DEC.)
Internal timing is important for in what order micro-programmable instruction will execute. (E.g., CLA will execute before CMA, so we can load -1 into AC by "cla+cma-opr".) But this may be simulated rather easily just by the order of conditions in emulation code, as the total execution time will be again 5µs.
While this should be good enough for basic emulation, like running visual code, there are probably much more complex interactions with various devices (e.g. magnetic tape and DMA, magnetic drum, etc.), which afford a much more subtle approach. I think, no emulator has gone there before and this is a really ground-breaking feature of Angelo's emulator.
A general observation::
I think, the role of the development and availability of power supplies and oscilloscopes (inspectability of voltage vs. time) is generally underrated. Oscilloscopes became only available in the early 1930s and the required power supplies became really feasible only after this. And, as these prerequisites fell into place, it didn't take long for computers or computer-like appliances to pop up. (E.g., Tommy Flowers began his experiments with tubes [brit.: valve] for switching in 1934 and had built a tube-based memory prototype for the British Post Office just before the war.)
Power supplies were a particular concern. There was a limited awareness in the 1950s that ternary logic may be more efficient (e.g., Wiener had discussed this in the late 1940s; compare also the report of the Engineering Research Associates Staff on High Speed Computing Devices, 1950), but I kind of doubt that this would have been feasible with the limitations of the power supply technology of the time, especially with large-scale tube computers. (Notably, the famous SETUN was solid state using ferrite cores for switching, which may be more than a coincidence.)
Best,
Norbert