Hi,
I have a 94 LS400 with air shocks/struts also. If you replace the shocks with coil overs, you should replace all 4 and pull the fuse to the pump. An alternative to the coil overs is Arnott Inc rebuilt OEM struts, or they also have a new Bilstein air strut replacement. Both have a lifetime warranty and are very good quality.
The problem you have now with the rear lines hanging loose is the system is trying to pump up pressure in relationship to the height sensors. You can try to plug the two rear air lines, or possibly remove the height sensor rods on the rear and extend them all the way fooling the system into thinking they are pumped up.
Best of luck!
http://www.arnottindustries.com/part_LEXUS...yid7_pid65.html