Instantaneous Movement to anywhere: Distant Shot feat + infinite spot check + permenant planar breaches + multiple bodies means It can see everything and throw Its bodies at anything It can see (made redundant by infinite speed)
Power Points: Metamind's Font of Power made permenant with Alter Reality
Melee Damage: d2 Crusader trick
Dark Crafting Gold: infinite Knowledge (religion) check result + a sacrifice (per the BoVD's rules on sacrificing). Note this can be set to any finite amount.
The area within Mechanus covered by his telepathy/mindsight (note that this telepathy doesn't extend outside of Mechanus at all): the
Primus's Telepathy + mindsight (see below for his telepathic range outside of Mechanus)
Telepathy and
Mindsight: the Psion(Telepath) ACF Telepathic Communication + NI manifester level + Mindsight feat + Extra Sense Enhancement divine salient ability (for good measure) (see above for his telepathic range inside of Mechanus)
Speed: the Living Ship's speed when being piloted + one body piloting another body + an infinite intelligence score + the Planar Shepherd's Planar Bubble(Su) made permanent with Alter Reality, set to any plane without gravity (note that the Living Ship's speed may need to be gotten with Fusion made permanent with Alter Reality since it does not have a listed ability type)
Physical attacks, individually targeted spells, and area effects have a greater than 100% miss chance against Pun-Pun (specifically a NI% miss change): Divine Dodge salient ability + NI divine ranks