Did you get the computer out of the manual truck. If not the computer in your truck still thinks it has the automatic and is not receiving a signal from the neutral safety switch. Also I would check and make sure you hooked all the wiring up correctly for the clutch pedal and transmission.
I think there's a way to by pass the neutral safety switch. But the truck will start in gear if you do that.
Also what all did you do, so we know what you did or didn't do as we have no idea what all you did.
2012 Chevy Silverado 1500 Crew Cab
1998 Mazda B-FORD-K: 4.0L | Auto | 4x4 | 244,000 miles
3" Body Lift | 33x12.50R15 Goodyear Duratracs | 31 Spline 8.8 Limited Slip | 4.10's
Super Lift | Coil Overs | Explorer Springs | 2" Shackle
FX4 Lvl 2 Seats | Explorer OHC | Full Length Center Console
C4x4 Front Bumper | 2006 Ranger Conversion | 15% Tint Over Factory
Recon 10.5K Winch | Headache Rack | Cobra CB | TG Rock Sliders | 200 Amp Alt