I had similar issues before, and it was really annoying indeed. On the top of it, for some reasons I was unable to make my flights IFR flights, so even though I was able to fly my flightplan, at night and bad weather, I had no chance to get permission to land.
Here's what I've figured out, and what works for me:
Make your flightplan in something other than FS2004, but in something which is capable to export flightplans both in the default fs2004 .pln file and the LDS 767's FMC format. I'm using FSBuild for this, always with the latest AIRAC cycle (current is 0801). For this you have to make sure that both FSBuild, and the LDS 767 has the same cycle installed to avoid any conflicts! For FSBuild you can get the updates with a few days delay from the current AIRAC cycle is released. 0801 is already available.
So when you have everything updated, make your flightplan in FSbuild (with the proper aircraft settings!) and export it with the FS2004/FSX and Level-D 767 formats. This way, both files will contain the same info. As a sidenote, I used to exclude the SID/STAR as well, as I'm using real weather which make the runways changing depending on the wind direction.
Once you have the files go to the FS built in crappy flight planner, enter the departure and arrival airports (or simply load your flightplan), then go to find route. And here comes the important thing! You must load your flightplan in the find route menu with the map displaying! It has a different result then! By this, your planned route gets to FS, with the most up to date navigation points and info! It's really important to load it like this, at least this is the only way I get proper results!
Then you select your aircraft, and at the departure airport you select your gate. Start, feed the flightplan to your FMC manually, or load the saved flightplan (co-route line). When you open the ATC window, you'll have to ask for the IFR clearance first, prior contacting ground. If you don't load the flightplan as I wrote, you'll have a VFR flightplan automatically by default, at least that's my experience.
ATC will provide info like you have to fly runway heading, initial climb 11.000 for example. You have to know, that FS does not handle SID/STAR at all. So even if you select it, don't expect ATC to vector you to follow it. In the real world they tell you which SID you have to fly on busy airports, but sometimes they just vector you to your first fix, skipping the SID or sections of it. ATC always have priority over your FMC data! As the default FS ATC doesn't know SID/START, in our case this is the case...you'll get vectors to your initial fix. Follow it, and they will tell you resume own navigation sooner or later during your departure, and you can follow your flightplan until you don't receive new instructions.
I don't think you can get any closer to the real stuff with the default ATC....This is the best I've found out. I hope it helps! It took 2 months for me to figure this out
If anyone else has a better solution, my eyes are wide open
Happy flying
Greetings, neu