My list of Pista upgrades: Flat crown threaded fork from Spicer cycles
Chris King "grip-nut" headset
Nitto chrome jaguar stem used with b123aa bars and aluminium pearl stem with rb21 bars
Nitto jaguar seat post
Brooks team pro saddle
Phil Wood track hubs
Velocity deep v rims (currently using gatorskin tires)
Izumi super toughness chain
EAI gold star 17 tooth cog and super star 15 tooth cog
Sugino 75 chainring, cranks and bb
MKS custom nuevo pedals
Toshi double toe straps.

I made these upgrades before any of the stock parts were failing, so I can't say that you should do x before y because I don't know. What I do know is which ones I feel like I couldn't ever switch back. That would be the saddle (which you've already upgraded) and the toe straps/pedals (a super plus to the straps if you aren't riding clipless). Comfort and security right there. On the non-essential side, I love having a whisper quiet drive train, makes riding more enjoyable. The wheels I love because I have only had to have one spoke adjusted (a 1/4 turn) after packing it into a hard case to fly with. Rock solid, those velocity rims. And that is with a non-standard lacing too, crow's foot in the back and alternating crow's and radial in the front. I can feel and appreciate the more powerful position the drop stem puts me in, but I could live without it (actually I do when I ride the bullhorns). I like the convenience of switching stems with the threaded fork/headset/stem to switch bars. The Nitto track bars are lighter in weight than the Dedas that come with the pista, so that's cool. The new fork looks bling as hell. I really have no reason to like the seatpost, 'cept it matches my bar/stem combo. Least important upgrade I made, I think. I still like it though.