I think you need to look at these balance problems very simply at first.
The problem is the wonder is WAY too powerful.
*25 gold per happy citizen across all your cities.
Solution:
Reduce it drastically.
*2.5 gold per happy citizen.
Im menzies this game and i have those two tokyo wonders that increase broadcast towers happies, so each broadcast tower gives me +10 happies (for example)
Each of my cities has an average of 44 excess happy people. (i have most of the happy buildings and pretty much every single resource)
so 44 times 2.5 = $110 per turn ( still quite a nice return

this is much more reasonable than $1,100 per turn per city)
$110 might seem alot but I am charismatic trait etc so it wouldn't normally be this high.
Problem no. 2 -
Encyclopedia - Free tech if 2 civs already have it - never expires.
Solution: Free tech if (total number of civs divided by 3 *rounded up!) has it. Also should expire with something like computer networks, you might also want to reduce the cost of wonder depending on its expiry time i feel.. These final decisions such as when it should expire or the exact number of civs required for free tech should be derived through play testing and feedback, but you really really need to start on the small side of things first.
Problem 3.
Spy costs - This needs to increase with each era- So in modern + transhuman era when I can easily make 10,000 spy points a turn, being able to bribe All TOP 5 CITIES OF THE WORLD for under 100,000 and still have change

is clearly ridiculous.
Solution-
Spy costs across the board (maybe something can be excluded) need to be increased by x2 each era. Something similar to this.. not sure exactly but at the moment bribe city and plant nuclear device, and force civic change(causing anarchy), religion change (causing anarchy), these are obvious ones that really need to be increased.
Honestly, I think Hydromancerx needs to look at any new wonder and introduce them to the game where they have the MINIMUM impact.
So using wembley as an example, it should start off at $.25 of and see how it affects gameplay, you don't start at the opposite end of the spectrum where these little things (such as wonders) can ruin the ENTIRE game..
Im not trying to be a d1ck or anything or sound ungrateful, but balance should be thought of as more precious than what it is currently.
Try and get a balance ---------- A steady nice balance --------- then introduce things to try and not disturb this balance ----------
Don't make wonders and buildings and units and hero units and great farmers and great projects that are superman powerful. Im not saying don't add these things at all, they are GREAT, im saying make them on the weaker side, and then see how you go..