Whenever I meet a new brew system, I do a water batch to rough in the set-up.
Starting with a full HLT, bring it to 200F. Calibrate a dipstick in whatever increments you like. I prefer using with hot water because of the expansion. At the same time, weigh your empty MT, with the false bottom in it.
Fill the MT with water up to the false bottom (I tend to go an inch above, because this would be my foundation water) and measure the loss at the HLT. In your equipment profile, this is your Lauter Tun Deadspace.
Add 50 more quarts of water to the MT and follow these directions (using 50 qt + deadspace as the volume) to determine your Specific Heat. http://www.beersmith.com/forum/index.php/topic,9324.0.html I'm using that number because 50# of malt is the nominal amount for a 1.050 beer and 1 qt/lb just makes the math easier.
Transfer 40 gallons water over to the boil kettle (or you can use the HLT if is has the same heat source) and bring it to a boil for 1 hour. This tells you two things: first is how long it'll take to get to a boil, second is the boil off rate per hour. Again, measuring at 200F will yield the most accurate results.
That should get you in the ballpark, quickly and take less than 2 hours. Trub losses, efficiency and the net yield, you'll just have to measure as you go.