Yes I'd say your cockerel is surplus to requirements. There's only one reason to keep a cockerel and that's for breeding and you shouldn't now be considering that with CRD in the flock also you shouldn't give any of the birds exposed to CRD to anyone else and don't introduce any new birds into the flock.
I'm very glad the infection seems to be working, that's excellent, but once it's all gone you just want to keep things calm and stable as much as possible and don't cause any upheavals like moving them or introducing new chx.
Although the infection started after introducing the L/S it doesn't necessarily mean they brought it in and more likely it was latent in the flock and the stress caused by disturbing the pecking order started it. I don't know if you have any exbatts but if so they could be carriers as a result of being vaccinated with a live vaccine for example, which is why I'd never mix exbatts with unvaccinated free range chx. You just don't know what they have been vaccinated with. Chx can be carriers but be immune themselves from the disease.
A few years ago when CRD was relatively rare I'd have said the same as Mimey and even now I cull if it apears in my breeding stock, but if you don't intend to breed from them or move them off your land this disease seems to becoming so widespread that A/Bs have to be considered as a pragmatic option. I'd suggest any that are left with permanent rales after the treatment you should consider as likely carriers and cull.
The eggs will be fine after the A/B withdrawal period as there' no danger to humans but don't use as hatching eggs. I don't know that even carriers shed the bacteria constantly in their eggs so perhaps some more knowledgable person might advise on this.
Regards