I installed new rotors and wheel bearings on the front of my EL about 2000k's ago, I would have thought that they would have had enough time to wear in by now but my brakes are still pretty weak. Any ideas?

Id bleed them and see how you go

Aren't ELs meant to bleed themselves?

Also how do you completely flush the system so that there is absolutely NO brake fluid or crap left in any part of the system?

Bleed one side at a time

how do you completely flush the system so that there is absolutely NO brake fluid or crap left in any part of the system?

Your problem will be the slides on the floating front calipers. Pull them totally apart, and clean thoroughly, rubbing with steel wool/scotch brite to remove any corrosion.
Coat liberally with copper kote grease upon refit. If the slides dont work, you only have about half your front brakes....
Then bleed the system, starting Pass rear, drive rear, pass front, drivers front.

Do not use Coppercote or any other antiseize compound that has oil as a base. This will make the rubber boots swell, on the caliper slides, and let water in.
Use silicone grease, can get that from Repco, or some bearing joints.
The silicone is water proof, and won't hurt the rubber.
To change flush the B/fluid, use a vacuum bleeder.
Clean out the B/M/cyl Res, put in new fluid, use the vac bleeder, to suck through the new fliud, do this again in about 2mths time cause the new fluid will lift the old crud stuck to the insides of the system, you may need to do this procedure about 4 times to get it to stay clean, depending on how long the old fluid has been it there.
The Ford factory fill of fluid is green, the stuff at Ford dealerships is blue. Thats how you know if its been changed at the dealer.
You may find the front bleeder nipples may be clogged with dirt/rust, this is common problem. There were no covers on them from factory, Why?, I don't know!!!???

We found copperkote was the only thing that worker back when I was working with the 2 XR8 Falcons in the Australian Rally Championchip.
Never had any problems with rubber swelling.

get your front discs machined and new brake pads quality paddss from bendix, brake pads that will not wear your newly machined discs

cheap brake pads have metal in them quality ones have better quallity bits