For water/ice/mud problems much depends on the route you chose. The graded federal road should not have standing water and has bridges across all rivers.
If you don't mind low temperatures, you could probably leave Magadan as early as May when it only gets -ve temperatures (C) at night.
If you want to use all the old summer roads you should leave it until July - ideally a little later.
On SibirskyExtreme we did the RoB from Yakutsk and Magadan in mid July 2009. The entire RoB from Yakutsk, using some summer routes, took us 3.5 days. A few short patches of mud and a couple of very small, shallow streams, but no real problems - other than mosquitos and my many flat tyres.
You can look up past weather records for temperature, rain etc for various months and years through here CLIMATE Magadan - Historical May 2009 - Weather
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