As stated previously I intend on adding this mod to the mod I am currently working on.
Glad you like Orion's Inquisition Mod and I think you will find it to be a fine addition to your mod.
Admittedly I haven't read the entire thread, but I had a few questions and concerns that I hope you can answer/ease:
No Problem.
I think the Holy Office building is way too powerful, and is it really necessary?
Right now The Holy Office is a required building to produce inquisitors. I believe this building fills a necessary attribute to help balance the game. Consider this: To win a religious victory, you must achieve religious unity. This requires missionaries to evangalize every city you own. Second, you must purge all non-state religions in every city you own. The cost of producing inquisitors can be enormous. Consider the cost of purchasing the Holy Office and an Inquisitor with turn 1 each under the Universal Sufferage civic.
Holy Office: Cost is
1080 Gold!
Inquisitor: Cost is
720 Gold!
Unless you have the Pyramids, you won't have Universal Sufferage early. So you are going to have to wait the equivallent amount of time in turns necessary to produce at least one Holy Office and then wait a few more turns to get an Inquisitor. The Inquisitor is by no means successful on every attempt to purge a city. You will have to produce many of them to achieve religious unity. Bottom line: you are loosing valuable production time and resouces (gold) that could have been used to produce combat units. Depending upon your situation, the failure to produce combat units could be a huge risk to the safety of your empire.
How do you offset this huge risk and expense? Enter the Holy Office, which provides 2 gold per turn. If you have 10 Cities, each with a Holy Office; then the income would be 20 Gold per turn. Using this income only, it would take 36 turns just to pay for one inquisitor and 54 turns to pay for another Holy Office! Assuming a high 70 percent success rate, conducting 10 inquisitions to clear out all of the non-state religions in 7 cities, would cost 7,200 Gold for the Inquisitors! Remember 3 of them failed to accomplish their task. Thats 360 turns to pay for the cost of achieving religious unity. However, by that time, you will likey have more cities to clean out. So the cost will be even higher. Yet there should come a time late in the game when you do break even and start to profit.
If I didn't want to use this in my mod would it be easy just to make a Cathedral requirement for an inquisitor?
Yes, but the game balancing effects provided by the Holy Office would be lost.
The Holy Office slows the growth of the city with -1 health, which is a big population hit, but not as big as loosing an enire population point.
The Holy Office provides +1 Happiness, as religiously unified city is a happy city all working for the same cause.
The Holy Office provides +2 Gold gold to offset the total cost of producing Holy Offices and Inquisitors.
On that same token can I give the ability to train Inquisitors without a Cathedral/Holy Office under Theocracy? (or is that already in effect).
It is possible using python, but I believe production of the Inquisitor should be based upon the Holy Office.
Can I alter the amount of money gained from conducting purges? It seems to me that this is also pretty powerful (especially after hearing about the amount of money you can make doing it). Can I take this out or limit this easily?
Yes, in two functions in the Inquisition.py file: RemoveAllNonStateReligiousBuildings and RemoveAllNonStateReligions.
The two gold from the Holy Office does not offset the huge risk of producing non-combat units. Your empire is really vulnerable during this time. Additionally, there is a huge risk of war, if you purge a Holy City and or a Shrine. With big risk must come a big reward. You get 500 gold for purging a non-state Holy City and an additional 500 if the non-state Holy City has a non-state Shrine. That's 1000 gold for risking war. ...not much when you consider what the war may cost.
For each religious building purged, you get 250 gold. This is a fraction of what it cost to produce these buildings. When these buildings are purged, the positive effects of each building is also lost, i.e. culture, happiness etc.
For each religion purged, you get 100 gold. Inquisitions produced a lucrative business during the middle ages. The 100 gold simulates pure profit from the confiscation of the victim's personal property.
Lastly, there is code to help an AI Civ convert it's cities to a new religion, if they finally get a Holy City. One religion per turn is given
free to the AI until all cities have the Holy City religion and the AI converts to the Holy City religion. This helps to even out the religions and makes it even harder to obtain the religious victory. You will notice this effect by the end of the middle game.
This stuff is relatively important because the mod I am making is meant for MP games, so if you just get money from conducting purges (with no negative, unless there is an I missed it) human players could just use that as a means to get more and more money, especially since the inquisitors don't purge missionaries (even then it would still be easy to manipulate). So I was just wondering if any of these issues are easily fixed/removed?
It can be done, but as I said before the game balancing effects would be adversly impacted. Remember, a lot of play testing has gone into this mod and it plays out very smoothly.
Respectfully,
Orion Veteran
If you have a state religion, there should be no reason whatsoever for building a competing Holy Office. The next release will definitely include this change. 
. I still think some further balancing of this building is in order. I would consider even making 1
instead of 1
And perhaps reduce the gold to just +1, while removing the 1
Could incompatible Inquisitors and Missionaries be killed off?
) for conducting an inquisition are now variables that you can set to any value you want! If you don't want any compensation at all, then set all four values to 0. These are the default values: 
