Tire seam.

It doesn't show very well in the pic and I had the camera on Macro mode. Maybe I should just finish the water grooves and call it good enough. The red lines show the insert of PVC and if you follow them up you can make out the seams. It shows more than in the pic.  

A real tire will have scuffs and groves cut into the tread. If it were me I would scuff the tire as it is being spun with some course sand paper....just lightly. This is a picture of a really well worn tire...

Aircraft tires go from 0 to what ever the aircraft is traveling at at time of contact with the runway...this subjects the tire to a lot of abrasion and heat instantly...so scuffs and gouges occur.

In addition to scuffing with sandpaper as I mentioned add a little weathering and you'll have  realistic tire. Mud covers everything...why do think armour builders swear by it and the use of tarps.

This's a motorcycle rear tire, right?

I'd cut the rest of the grooves with a razor saw, then scuff up the tread with coarse sandpaper like Gerald said.. I think after the paint's on and weathered, that stuff you're having issues with disappear, or at least be camouflage so well noone will notice, and especially if you hide the worst part either at the bottom or under the fender..

Yep, it's supposed to be a rear motorcycle tire.

Thanks for the help guys. I just filled a few spots this morning and will sand it tonight. Then start trying to cut the grooves. That in itself will be fun to get the curves right. When done it might look like a Metzler. I'll post a pic when done.

I thought of a way to take care of that seam if you've got the casting recources to spare...

Fill the seam, but leave the filler above the seam, keeping a ridge where the seam was; that is, don't sand it smooth.  
Cast the tire in resin, including the new ridges.
Take the new resin tire to the lathe and sand off/remove the ridges that are now in resin.
You're left with a smooth tire with no seam and no ridges. Now you've got your perfect master pattern.

I hope I made sense. I know it's not the most economical way to go about it, but it will probably yeild the best results with the least effort.

I understand what you are saying and it is a good idea. That way it would all be the same media and would be easier to work with.

ETA: While taking the thing out for another coat of Mr. Surfacer, it fell, hit the floor, and one side went flying. I did find a spot to index it back together again, so it's just a hair line crack. Soooooo.....back to filling and sanding. I needed to get an engraver bit for the Dremel anyway.