A few questions

I have been attempting to fly a fictional Federal Express cargo route as realistically as possible. Have had some problems with starting from a cold start and losing my IFR plan with FS2004 so ATC will work right along with my FMC. What is the best "pre-flight" so to speak to load up cold and fly, I realize i need to be in flight before I can safely save my in progress flight. I have read about the save Cessna cold, with avionics on so my radios will stay working, also bound the master avionics on key to something, though the bus dc volts are low sometimes keeping the ATC from working even though NAV and adf do work. My fictional flight is based on a Fed Ex Airbus that flies out of KMHT at about 1:00 am (-5 gmt) after being loaded, I figured it may be heading to KLAX for AM next day air? So Its KMHT cargo 23 ramp for KLAX. I start by getting all my weather data. Question: What region should I use for my Flight CRZ Altitude wind dir/kts and temp? I have been using the NE weather data but most of flight is over mid US. Have been using weather.noaa.gov for weather reports.Question: I create an FS2004 IFR flightplan for KMHT and KLAX, then load fuel, then I go into the cold 737 using only grd power and program the FMC using those waypoints and correct 2 that register 4k distance incorrectly. Then I save my flight, if I leave and come back after saving that flight as default have I lost my IFR plan with ATC in FS9?Question: What cost index would an overnight cargo carrier use, or a best guess? And can someone give me a revised checklist for a cargo 737?Also I realize the patch will fix the radios/power problem.