I had tried GT5u with TFC a while ago and had no issues with ores and ingots. If I get time after work I'll look back through my old videos and see what I can find. My issue with doing it was crop sticks not working on TFC farmland and at the time there was no nether to spawn GT ores in so I was using custom ore gen to spawn small GT ores. Then I had a bad chunk error that ended the series and haven't gotten time to get back to it since the changes to TFC.
Hmm that's a thinker then. Really the only other core mods I am using are Railcraft, AE2, and Immersive Engineering. Can't imagine these would affect anything, but maybe I will test.
I got frequent chunk errors with custom ore gen & TFC even in their most recent iterations, so I nixed custom ore gen for the time being and used some of TFC's unused ores, which already generate, as replacements through minetweaker. Apparently you can add ore to TFC's generation through the TFCore.cfg too, just not tile entities like GT uses, so I will probably employee this hackery at some point to make the rest of the tech tree accessible.
Just trying to fix this problem at the moment though.