Hehe, those changes were in a plain text file, the definition files in \Tables. This is about the xml files, in \Data. [Just checked it, and now they are dead

]
Got your PM, will check it tonight when I get home. Meanwhile, here's some more stuff from the previous versions, stuff in that huge post I mentioned that wasn't fixed, and stuff concerning the previous fixes. Some might be intentional (not to fix), some are definitely not. It's a lot of stuff, I'll let you sort it out
Type 1 University is producing 12000 research (instead of 12). Probably a leftover from testing.
Research Matrix
In level 4 techs for the Dominion, unlocked techs include the Type 4 University (Federation).
Trade Centre upgrades to Trade Hub, but Trade Hub does not obsolete Trade Centre. They shouldn't be cumulative.
Trade Centre doesn't have any restrictions (which makes Trade Hub not have too), should probably have OpS (in case the default OpS is fixed). Same happens with the Fed Replicator Plants.
Starfleet Intelligence
Doesn't have the One Per Empire restriction. For consistency only.
ASDB Complex
The Dilithium restriction is a bit redundant because Sol has the Dilithium bonus by default. Even if it were made not to have, then the facility wouldn't make sense.
Same thing for the Dilithium Cracking Station of the Coridan (BTW, its description text sounds more like a first contact text than the description of a facility of a race which *already* is allied with you...)
None of the universal scanners have the OpS restriction (besides the default).
If I conquer a system with a top of the line scanner, I cannot upgrade it to my own empire's top of the line scanner, right? It's a bit odd, them obsoleting all the others.
Cardassians cannot upgrade a Listening Post to a Card Listening Post (in case of conquest for example). In fact the former obsoletes the latter. Same thing happens with the Isolinear Scanner and Card Isolinear Scanner.
Aquasphere
The description mentions a Biotech research bonus; Statistics says +100 Research (global) though.
Planetary Shield doesn't have the OpS restriction.
Starfleet Academy
It's a OpS and OpE facility, shouldn't it also have the Home System restriction?
Subspace Jammer doesn't have any restrictions.
Fed Global Defense Net
No restrictions whatsoever. Should probably have OpS (in case the default OpS is fixed).
Should probably give an Anti-Ship Defense (-> Defence) bonus, and not a +% Anti-Ship Defense - if there isn't already an ASDef value, GDN does nothing, and its description sounds silly (and misleading).
(Elaysians) Low-Grav Resort
The Non-Native System restriction should be removed.
Some structures are set to not be universal, but they're not in any empire's techtree: Aquaculture Centre, Commerce Centre, Commercial Exchange, Commercial Hub, Subspace Jammer.
(The Aquaculture Centre could actually help the Romulans at game start)
Card Obsidian Order
Is still missing the One Per Empire restriction.
Card ReEducation Centre doesn't have any restrictions.
Rom Reman Dilithium Mine doesn't have the OpE restriction.
Rom State Broadcast Bureau should probably have a native System restriction (OpE).
(Klingon) Great Hall
Should it have the OpE restriction?
The Cardassian Relocation Project has energy cost 200, and restriction NonNativeSystem, while the Romulan and Federation equivalents have zero and Moons respectively. The Klingons and Dominion don't have these?
(Klingon) War Room
Is it supposed to only have the OpS restriction (default)?
(Klingon) Forced Labour Farms
Should also have the Conquered System restriction, like the Foundry?
The Klingon and Fed Apothecaries don't have any restrictions.
The Combat Grid (minors) should get the OpS restriction, or you can build as many as you want (in case the default OpS is fixed).
The Cardassian Union Broadcast Network doesn't have any Restrictions. Besides the OpS default that is, but if that is fixed, it isn't restricted in number. Since it grants +1 morale empire wide, even the OpS might be a bit much.
The Klingon Mark 1 and Mark 2 Replicators don't have an upgrade/obsoletion link. They also have no restrictions. They're worthless because of the Basic Food Processor, which is supposed to not have any restriction, and is much cheaper and consumes much less energy.
Shipyards (level 1) should get the OpS restriction. They should obsolete the minors shipyards too (Romulan already does).
Minor Advanced Shipyard is available at tech level 8 instead of 9.
Is it intended that the Cardassian shipyard III has energy cost only 75 and 6 build slots? A bit inconsistent with the respective fleetyard.
Cardassian Colony ships still don't upgrade.
Bolian Freighter II doesn't obsolete Bolian Freighter I.
Breen BattleCruiser III is obsoleting Breen BattleCruiser II instead of Breen BattleCruiser I.
Coridan Cruiser II is obsoleting Coridan Cruiser I.
Minors:
Acamarians
They're described as "With the military infrastructure that they have, they are more than capable of defending their homeworld.", and they're considered Developed, but their techtree only includes the Civilian Reserve and Resistance Cells defensive techs (plus the Orbital Batteries).
Algolians
Should the Algolians be Backward techwise, with the minor structures they get (compared to other minors) and the gift for intellectual capacity they're described as having?
Cytherans
They're supposed to be made of pure energy, but they can build all of the defensive structures for minors (probably because of the Supreme tech rating).
HomeSystems.xml:
Arbazan
Arbaza I should be called Arbaza, according to the race's description.
B'Omar
Their homeworld: Bomar

B'Omar
Ba'ku
Their homeworld: Ba'Ku

Ba'ku
Elaysians
Elaya III should be called Elaya, according to the race's and Low-Grav Resort descriptions.
Ferengi
Races.xml, is their homeworld really supposed to be the Oceanic planet, or should it be the Jungle planet instead? The system has both set as mandatory.
Yaderans
Swap homesystem (Yadera Prime) and homeworld (Yadera) names.
Races whose Inhabitants are set as Humans:
Baneans, Malcorians, Mintakans, Pakled
Races that don't force the class of the homeworld:
Bothans, Coridan, Dosi, Sheliak (system has no planets AT ALL)
Star system name and type not defined:
Tilonians
Unnecessary <Planet /> tags (probably leftovers from editing):
Zibalians, Ventaxians, Ullians, Tilonians, Tanugans, Talosians, Takarans, Sikarians, Rutians, Ramatians, Wadi, Trill, Tholians, Tellarites, Son'a
Systems that can have more than 10 orbits:
HomeSystems.xml
Bre'ellians 10~11 orbits
Coridan 3~11
TechTrees.xml
The Axanar, Coridan, Kazon and Tellarites shouldn't have the Basic/Medium/Advanced Shipyards, since their special shipyards are supposed to obsolete them.
The Alsaurians have shipyards but have no ship designs.
The Brekkians have one ship design but no shipyards.
TechObjectDatabase.xml / TechTrees.xml
For easier reference:
HYDROPONICS_DOME

CARD_HYDROPONICS_DOME
FREE_MARKET

FED_FREE_MARKET
PRIVATE_FARMS

FED_PRIVATE_FARMS
HOLOCENTRE

FED_HOLOCENTRE
AGRICULTURAL_CENTRES

FED_AGRICULTURAL_CENTRES
Ships:
All ships should require at least Propulsion 1, which is the Warp Drive (probably Construction and Weapons 1 too, while at it). The Outpost I should also probably require Construction and Weapons 1.
Federation New York Class
Upgrade Options reads Berlin Class (which is the predecessor, Obsoleted Item).
Dominion Battle Cruiser III
Has Range = 0.
A bunch of Cardassian ships have no Dilithium cost.
All Cardassian colony ships have no Work Capacity set, that's why they can't colonise. The Federation Colony Ship III has the same problem. It's easy enough to fix (TechObjectDatabase.xml).
I was under the impression that you said that Federation colonies were supposed to be the best, but the Work Capacity of their colony ships is actually the worst (25 vs 50 for everyone else in Colony Ship I, 50 vs 100/150 in Colony Ship II). That means the colonies start with not only half the pop of others, but also half the initial structures (as they're related).
The Romulan Transport Ship II has Work Capacity = 50 (same as the I), it should probably be 100 like every other empire (the III has 150).
The Colony Ship II for the Klingons and Dominion (they don't have the III) have the same Build Cost (approx.), Raw Materials and Crew as regular IIs, even though they have the Work Capacity of IIIs (and are armed). Maybe an intermediate value?
The Federation Colony Ship I has a value for Population Health, no other colony ship in the game does. Intended?
The Romulan Colony Ship III is a bit on the cheap side, when compared to the others.
Acamarian Raider I: are the Scan Power and Sensor Range values switched?
Angosian Transport: no Crew.
Bilanaian Destroyer: no Tech preReqs, Type = Colony.
Boslic Transport II: no Dilithium cost.
Breen Battlecruiser III: ClassName = Breen Corasta Class

Corasta.
Brekkian Transport: no Tech preReqs.
Bynar Cruiser: Type = Colony.
Caldonian Explorer: Type = Colony.
Denobulan Frigate: Range = 0, no Maneuverability value.
Dosi Cruiser: no Tech preReqs.