I'd go with the new 9-speed 3500 Sora (or Microshift) shifters and limit the other 'upgrades'. For example; brake pads instead of calipers; cassatte, chain, and cables/housing but likely not derailleurs; etc. But it's your money.
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"The older you do get, the more rules they're gonna try to get you to follow. You just gotta keep livin', man, L-I-V-I-N." - Wooderson
'14 carbon Synapse - '12 CAAD 10 5 - '99 Gary Fisher Big Sur