This new tusq saddle sounds good to me. But, I know the intonation isn't perfect. But, I don't hear any problem when I play. Most of my playing is on the first 7-8 frets. So I have some options.
1. Shut up and play and don't worry about intonation until I can hear a problem when I play.
I don't care much for this option because even if I can't hear anything wrong when I play, knowing the intonation is off is a downer. Plus if I ever play the higher frets there may be an obvious problem then.
2. Put the bone saddle back in because the intonation is perfect or at least almost perfect.
Forgetting about intonation, this option also has the benefit of giving be a better idea of the difference in sound from the bone and tusq saddles.
The following options involve me filing a saddle to set the intonation myself. I have never done this before. I think I understand the concept and it seems pretty straight forward. Having said that it seems like it would be easy to file a little too much if I get in a hurry. Even so, right now I have two perfect Ibanez stock saddles and on perfect bone saddle to use.
3. One option I can take is to file the tusq saddle I have now to correct intonation. If that lowers the action on the lower (pitch) strings I could use shims to raise it back up and re-sand.
When I bought the bone saddle I also got a few shims. I believe I need to glue them to the bottom of the saddle and re-sand for action. If different materials (bone vs saddle) create different sounds, will using shims change the sound? The shims are ebony. Probably one of those things I won't know until I do it.
4. Get another identical saddle and file it first to what I think would be good intonation. I would do this by trying to shape the top just like the bone saddle. Then sand the bottom to set the action.
Actually, this sounds like the best option if I want to keep a tusq saddle. I'm also thinking trying to get the other tusq saddle perfect (or close) using shims if I need to will teach me more about the whole process. What I mean is my existing tusq saddle would possibly be for practice. If I need another new saddle maybe I would have learned a bit and not mess that one up. 
I'm going to do something with this but I'm in no real hurry. I'm going to read or re-read a few things on internet sites or look at youtube videos before I get started. If anyone has any tips or suggestions I'd be very grateful for any help.
As far as tools go I have a Dremel as well as clamps, vises or anything needed to hold the Dremel or the saddle still. I'm pretty sure I need to stay away from any tool using a motor when setting the intonation. I used my bench sander to remove a lot of material from the bottom of the saddle. But the last bit of sanding I used a diamond sharpening stone. I also have sandpaper from 60 grit to 2000 grit. I have needle files. Nothing like you might need for filing string slots in a nut but plenty small enough for filing a saddle. Any help is appreciated.
Jack