I did a mini ape set on my 2003 fatboy. Ran the wires internally. my issues is the turn signals don't work on wither side. all other buttons work on the controls. I have checked the fuse and it is fine. the running lights are on, and the bulb is not blown. I don't have anything pinched or so it seems. they worked fine before. could it be the switches themselves? Please help

 

Doubt it's the switches, maybe you've got a bad connection to the switches.

 

Good chance when you pulled the wires through the bars it may have pulled your connections loose. Or, when you put the tank back in position it has pulled the wires loose from the connector sockets.

I've had to run down BOTH issues in the past after doing bar swaps.

 

I know you said you checked for pinched wires, but just sharing my experience...
Same thing happened to me once, turned out to be a pinched wire when I tightened down the switch housing. Loosened the switch housings a tad from tight and everything worked, tightened switch housing down tight and everything worked except the blinkers. Actually one blinker light wouldn't even light up.
My issue was because I cut the bar ends an inch and it was just enough that the deep part of the dimples didn't line up quite enough with the switch housing end. What I had to do was file down a little part of the housing where the wires come out so it lined up with dimple part so it wouldn't pinch.

I know not same scenario for you, but would look for a pinched wire somewhere down the line. Loosen and tighten from switch housing all the way back.. worth a try