I'd say that Makhnovschina should not exist at the start of the scenario. However, make sure that both event 48100 (February Revolution) and event 69001 (Ukraine is free) are included in the history = { } section of the scenario .eug file, so that the random event creating Makhnovschina can activate later.
Historically, Makhno was leader of the Gulyai Polye Soviet at this time, organising resistance to the Germans and their puppet Ukrainian government. However, it wasn't until January/February 1919 that he set up an actual government with an army.
Rumania should not have an OOB. (Technically, the Germans allowed them two understrength divisions with just a few bullets per rifle to act as internal security forces, but I don't think this is worth representing in the game)
The Soviet fleet was described in one of my earlier posts (154, I think). Basically, they had about half a dozen operational ships left over from the Tsarist navy, plus a few more which were in a hopeless state of repair and so should start the scenario at strength = 1.