According to these old pictures of mine and a rusty memory, you'll need to remove the old Toyota u joint and install another one that adapts it from the Toyota driveshaft to the Dana 60 yoke (should have also sent the u bolts for the new yoke). This should have come with the new axle from ECGS. I had no clue how to do this, so luckily my buddy helping me did and without screwing it up we were able to pull it off. According to him there is a danger with the little needle bearings falling out and not getting positioned correctly.
I have the old boxes still, type these into google you'll find some pics.
(1) Spicer U-bolt Kit 2-94-28X
(1) Powertrain Industries 1351-31 (ECGS #U-TOY-MITS-1310)
And according to this pic, the axle came with hard plastic spring isolators that have a lip you use for the first coil, though I don't believe these isolators were actually attached to the axle, so the springs could still spin around. Maybe ECGS doesn't include these anymore, I'm not entirely sure what they do.
As for the stock sway bar fitting, I've never tried. Does it not fit over the hump in the middle?