Out:
Negate - Replaced with Arcane Denial
Trading Post - Mostly used it to recover combo pieces from my graveyard. Replaced with Codex Shredder.
Arcum Dagsson - Has to stick for a round, plus has to have an artifact creature on board. Replaced with Reshape.
Vindicate - Usually too slow.
Trophy Mage - Replaced with Whir of Invention
Mountain - Replaced with Spire of Industry
Sram's Expertise - Doesn't do enough. Replaced with Second Sunrise
Stoic Rebuttal - Replaced with Swan Song
Mycosynth Lattice - Wasn't really useful anymore, except for the combo with Vandalblast

In:
Arcane Denial - Unconditional counterspell with downside, wider than negate.
Codex Shredder - Part of an eggs combo I'm planning to include, and does the work of Trading Post better.
Reshape - Puts an artifact directly into play, good for toolbox use, acts as a ritual with Lotus Bloom (will be added)
Chain of Vapor - Instant speed nonland removal. Testing in place of vindicate.
Whir of Invention - Can get a combo piece on instant speed, can put lotus bloom directly into play.
Spire of Industry - Taps for all colors + colorless
Second Sunrise - Part of the Eggs combo
Swan Song - Narrower than Stoic Rebuttal, but a lot cheaper.
Chromatic Star - The best of the eggs.

Out for testing purposes:
Wurmcoil Engine
Scrap Trawler
Wrath of God
Vandalblast
Basalt Monolith
Dig Through Time
Ashnod's Altar
Windfall
Muddle the Mixture

In for testing:
Chromatic Sphere
Paradoxical Outcome
Implement of Combustion
Faith's Reward
Foundry Inspector
Ad Nauseam
Scrap Mastery
Terrarion
Unsubstantiate
Implement of Improvement