It sounds like you are now on your way to a harmonious household, but just to answer a suggestion from an earlier post, I have seen Feliway help in these situations.  A friend of mine just went through something similar where a new male cat started attacking the other male who had been in the household for a longer period of time.  Nothing was physically wrong with either cat so the vet suggested Feliway and they put the diffusers in each room that the cats would hang out in.  It helped almost immediately.  I should add as a word of caution however that because Feliway is pheromones sometimes males have the opposite reaction and start demonstrating more aggressive behavior and even spraying.  Most of time it seems to help, but I guess it depends on each individual cat.

Update on Linley’s behavior and integration with the other cats—

We kept him completely separated from the other cats again until about 10 days ago.  (We were doing the various scent item exchanges, and putting Rescue Remedy in his water through this time.)  At the first re-introduction session we had 3 “responsible adults” in attendance, and carried Linley into the main living area where the other cats were.  One person was armed with a spray bottle, one with a handful of cat treats, and one was the general go-between.  Instructions were that someone should be next to Linley at all times in case he attempted to attack, and stay between him and any other cat.  Another would intervene with the water to drive him off if he did.

This first session was beautiful to see.  There was much mutual nose-touching and rear-sniffing between Linley and Cameo.  They looked like long-lost friends.  We were handing out cat treats all around like crazy to reinforce calm, appropriate behavior and promote a general feeling of well-being.  The other 3 cats seemed a bit edgy, but showed no other reaction than to keep their eyes on him.  Linley did normal cat stuff.  This lasted for about 1 ½ hours, and then we put him back in his room.

Unfortunately, subsequent sessions did not go so well.  A certain family member (who, if I had a dog, would have spent the night in the doghouse!) let Linley loose on his own later that day without anyone else available to monitor carefully (I was cooking dinner).  Apparently Linley ran up the stairs and Cameo took a swat at him as he ran past.  He attacked her.  She screamed and went into full defensive position, all claws and teeth, as he went for her.  Spray bottle on Linley, chaos, scared cats all around.  Linley back to exile.  No physical injuries that we could find, but much emotional trauma.

We tried another brief controlled encounter again that day, after all had a few hours to calm down, to try to erase the memory of the bad scene.  We held onto Linley the whole time.  Cameo was hissing like a cobra.  Kalahari and Phantom took one look at Linley and fled.  Since there were no actual attacks, we did give treats to Linley and Isis, whose behavior was appropriate.

Since then, we have taken another tack.  Cameo has been allowed into Linley’s room while someone is holding onto Linley, for brief periods, at her own initiative.  He has not tried to attack her again, but does sometimes struggle to get free.  She and Linley are also occasionally observed playing a game (at least, I hope it's a game) of batting each other’s paws under the door of Linley’s room.  We have also been giving Linley nightly “run sessions” each evening when possible, where he has the freedom of the house and the others are enclosed in their own areas.  He consistently seeks out the room where Cameo is for part of this time to play the paw game under the door with her. We also still spend plenty of time with him alone in the office every day.

Linley did get out accidentally again once, and immediately charged Kalahari, who happened to be in the area.  Fortunately, she is fast and agile and can find places to hide.

It’s turning out to be a long, slow, labor- and emotion-intensive process.  Some days I feel very discouraged.  If Linley weren’t such a nice cat, who seems so eager to please when the others aren’t there, I would have given up by now.

 ;)This will sound INSANE... but It was suggested by a lady who has done feral rescue longer than I have been alive and it worked for my then 16yr old Kandie and Zoey who turned out to be 8 months and feral...

Get a drop of vanilla ( the real stuff) and place it on noses and rears so everyone spell s the same.. It too only two times and life was CIVAL again at my house

Keeping my fingers crossed...
Linley seems much less high-strung and desperate to get out of the room this week.  He seems to have slowed down.  Maybe it's the nightly run sessions; maybe it's that more of the tomcat hormones have left his body; maybe it's both.  Usually now when I feed him in the morning he just wanders a few feet out the door of the room when I enter, but comes right back to attend to his food dish.  Today he did this when Kalahari was in the next room.  His ears and head went up, and he oriented towards her, so I was afraid of another chase--but when I called him to his food, he just came back to that.  I petted him and told him he was a very good boy.

A couple of nights ago we tried putting him in a crate in the room where we were sitting with the other cats.  After about 15 min. Cameo stopped hissing and was just watchful.  The other cats seemed to benefit when they realized he couldn't attack.  But it did not work well for Linley himself.  He cried piteously and tried to dig his way out of the crate the whole time.  He made his nose sore from pushing so hard on the crate bars in an attempt to escape.

Wonderful that all your efforts are slowly paying off catbird!  You are a very patient pet person (VPPP) to keep it up this long.  Linley sounds like he's worth it though!

Catbird- I agree,once you have them they stay.Glad things are improving even if its slow.

Sounds like good progress with Linley and the girls.  Patience will be rewarded eventually.