long stroke + small bore = better set up for TQ as opposed to HP. short stroke + large bore = better set up for HP as opposed to TQ
If you look at the V-8's that are high RPM performers (BMW M3 for example) they have a short stroke and large bore.
4.6 Ford bore and stroke = 90.2 mm and 90 mm
BMW M3 V-8 bore and stroke = 92mm and 75.2mm
There are other factors as well. In the Mustang the intake manifold has long runners which promote low end torque at the expense of high RPM hp, the heads were not designed to support high 5000+ rpm HP, the cams were designed to be daily driver friendly and provide a broad torque curve, they didn't come with headers, the exhaust is quite restrictive (especially the mid-pipe), etc...
The heads/cams are basically limiting the breathing potential of the motor. Get some ported heads and some bigger cams in it and it will pull well past 6k rpm.