2-3 Second recycle time is based on a full power dump from the D1. If you lower your flash power to around half power, the D1 can keep up with your 7D firing at 3 fps. I shoot my D1's at just under half power and it keeps up with my 5dmk3 at 6 fps.
Of course, good NiMH cells (Maha Powerex) help too.
There's no point in shooting full power on your pop-up flash when shooting in manual, you just need to trigger the D1, then control strobe power on strobe.