You should't have a problem running shorties. They are the same size as the stock manifolds. But you will not see any gains going from the stock manifolds to shorties. The Schoenfelds are going to give you a much better gain. They are only $270 uncoated. You can also use pacesetters for a 99-06 truck.
SOLD:1992 ECSB Silverado lm7 5.3 Swap, TR220 cam, Circle D 3200stall, CBM street tune, Schoenfeld LT's, LS1 efans, transgo hd-2 60e, custom CAI, Autometer gauges
Best 1/8 E.T. 8.86 @ 77.8 on 275/60/15 MT ET Streets with 1.92 60 ft.
2000 RCSB 4x4 Lq9 swap...stock except mild 4l65e....for now