Hi Andy, list of upgrade priorities can be quite long and also become expensive and have listed below what I reckon would be best bang for your buck.

Replace nut - DB's bone ones are not cheap at around $28 but you know it will be top quality compared to $7 eBay specials
Replace pots & tone cap - if keeping the 2 x vol & 1 tone do not do the treble bleed mod as it does not work too well in this setup
Buy some decent strings - a set of D'Addario round wounds are my preference and by selecting slightly heavier gauge 50-105 discovered standard bridge did not have enough fore & aft travel to get correct intonation but worked ok with 45-100 cost $36
Replace PUP's - went cheap with the Entwistles but chose their dearer high spec ones. Tend to think Tonerider is better
Replace bridge - standard one is just ok and bought economy Gotoh style for $28 from Real Parts
Replace Tuners - under tension you may feel the gears slipping a smidge when tuning up - try Real Parts/All Parts USA set $48

Ultimate upgrade list amounts to around $280 plus freight from the various suppliers. On PUP's the high spec Entwistle set is only $30 cheaper than a Tonerider set however they do have cheaper ones which for a pair are about the same price as one Tonerider and would definitely be a whole lot better than the stock units.

As others have already said bridge doesn't affect the sound as much as PUP's and can be done later. Just be mindful what I mentioned about heavier gauge strings. They sound better but you may find standard bridge lacks enough room for adjustment to properly intonate.

Cheers, Waz