I have a NP435 with a Dana 24 transfer case coming off a FE 428 in my 72' F250 bump, there is a new noise that sounds metallic and whinning when I am in 3rd gear. The truck drives smooth and shifts fine, but the noise is worrisome. What are the things I should be looking at or for to figure this out. Thanks

 

Without getting into a flame war with others stating the 435 being the strongest box around and i'm just flat azz wrong, they will fail under higher hp and torque especially if you hammer on it. You want to feel sick put your ear on the shift **** in neutral and again in 3rd gear at 15 mph.
The mainshaft with input taper bearing one end and ball bearing are a miss match to each other. That 308L ball bearing only has 7 ***** I knocked 'em out many times until replacing it with a 11 ball bearing making it 57% stronger. My suggestion when rebuilding a high mileage unit of over 600K miles is check the cluster gear end float, I find the thrust washers (bearings) will not tighten up this clearance. I ended up refacing the thrust on the cluster gear and adding a spacer between the case and standard thrust washer. Check the roller bore in the cluster as well shaft and rollers.
On the input and retainer new taper unless it's perfect. What I have done is set the synchro clearances .010" below minimum spec for sooner synchro action (there are shims for this)hence no crunching even when speed shifting, yes I hot rodded my old truck with a 414 motor. A new or tight no slop shifter top makes shifting a pleasure. Everytime the top is off change those nylon shifter fork pads. Later style shift lever had "O" rings isolating the gate pin from the shift lever for les noise and vibration causing less postive synchro action, slop and feel whats going on when you shift. I replaced the "O" rings with epoxy. Same thing with those loose pins locating the shift lever ball, I tap and threaded allen bolts with the thread machined off where it contacts the ball slot for a close clearance fit. If it's loose it doesn't feel good (don't tell the wife).
A good pressure plate not some cheap reman or cheap new one that has a thin gauge basket vs thick basket, they will crack and come apart under higher torque use like your 428 will deliver. New pilot and disc a must, hate clutch chatter. Check the disk on the input shaft for wobble before installing.
Nuff said this what I did to keep a 435 together for over 922K 34 years of hard miles, new truck owner past the million mile mark 3 years ago.
There will be others smarter than I with answers, if so totally disreguard any and all of this post, what the hell do I know?