tb breather , valve cover fiasco ??

That is pretty stange. You'd think it would work the same as the stock setup.

Whatever you do make sure the crankcase has some way to breathe... The PCV is pullling vacuum in the crankcase, but it needs to have a way to replace the air thats being pulled via the PCV, and thats what the TB to valve cover hose is for. If you like these valve covers and are hell bent on keeping them, then install a K&N type breather on one side or something. If you dont do something to allow air to get back in from the PCV sucking it aout it will start to pull air from the seals or wherever it can.

My 65mm T body had no provision for the hard line that runs to the stock valve cover. So I plugged the nipple on the oil fill tube and the car developed a loud squeal which was air being pulled through the front seal. Drill provision in 65 mm T body, and installed the metal tube and plastic line and alls well.

Try finding some stock valve covers...

I run carb motor covers on my car, with the tube attached. Ford Racing sells a breather that's closed, and has the nipple on it so you can hook the tube up. As far as your problems, I'd reset the computer. It might have learned to run with all that extra air from the PCV, and now it's richening up. That, and make sure the oil baffle is in the new covers so that you're not drawing oil into the intake.