1) Did you replace the caliper hoses also?
2) The replacement 'stainless steel lines', are they 'hardlines' or 'braided flex (hose)'?
3) The deletion of the ABS, did that create a 'high spot' in the lines, whereby air might be trapped?
[and for what it's worth, I personally think you're already on the correct diagnosis with it being air still trapped in the system]
1992 YJ, 401 V8, EFI, TH400, Atlas, D60s, Detroits, Warn 8274, Cage, 37 Krawlers
1997 TJ, 350 V8, EFI, TH400, Atlas 4spd, D60s, Detroits, Warn 12000, Cage, 40 Kevlars
TTC 1994, TTC 2012, Trail Tour participant.