Since I can not store the bike, I have been riding whenever the temperature as above 40 degrees (nyc to be exact).

I have not taken the bike out since our last 50 degree day in early december.
Just took it out today and when I started the bike, the engine or starter clanked (since it was a big thug, my guess is the engine). How do I prevent this in the future? Guess the engine wasn't properly lubed after a few weeks of sub 30 degree weather (and lower). Is there an additive I can put into the engine so I have minimum lubrication for a smooth cold start?

Switch to Amsoil's Formula 4-StrokeŽ PowerSports 0W-40 (http://www.amsoil.com/StoreFront/aff.aspx) synthetic oil (JASO MA certified). I use it year long for our relatively cool climates. It has a -51°C (-60°F) pour point, yet with a slightly higher viscosity than their 10W-40 motorcycle oil at operating temperature. You can get it from http://www.woodsbrosracing.com/amsoil-online-store.htm at 20% off with secret promo code...
For now, try pre-warming the engine somehow with a small heater or heat lamp underneath for an hour or so before starting it.

Since I can not store the bike, I have been riding whenever the temperature as above 40 degrees (nyc to be exact).

I have not taken the bike out since our last 50 degree day in early december.
Just took it out today and when I started the bike, the engine or starter clanked (since it was a big thug, my guess is the engine). How do I prevent this in the future? Guess the engine wasn't properly lubed after a few weeks of sub 30 degree weather (and lower). Is there an additive I can put into the engine so I have minimum lubrication for a smooth cold start?

did it start right up after the noise probably the starter sounds normal to me...starters kick back when motors turn over hard from cold..low battery ect..thinner oil weight might help...