Check out the
SEIV Modding 101 Tutorial for a good introduction to modding SE4. It does not explicitly cover AI modding, but it covers the data files.
You can use the mod you have made now. Edit the AI Research files for each AI. They are located in the Pictures\Races folders. There is also the default research file in the AI folder, which is used by races without AI files and by neutral races. I recommend that you do not modify the stock data or AI files. Instead, create a mod folder, such as MyMod. Duplicate the stock game file structure in there, for the folders that contain files that you modify. You only need the modified files in the mod folder, except for the Data folder, which you need most of the files. Just make a mod folder and copy the Data folder (including the folder) into it. Create a Pictures folder, then a Races folder inside it. Create folder for each of the races in the stock game, 20 in total. Copy the AI files you will be modding into the mod folder, and modify them.
As for getting the AI to research Applied Research first, you will want to add something like this as the first entry in each AI_Research file:
AI State := Exploration, Infrastructure, Prepare for Attack, Attack, Secure Holdings After Attack, Incursion, Prepare for Defense, Defend (Short Term), Defend (Long Term)
Tech Area Name := Applied Research
Tech Area Level := 1
Tech Area Min Percent := 100
This will cause the AI to select Applied Research as it's first tech project.
However... it is not a good idea to not have the AI start with a SY facility. As you have noticed, they do not scrap facilities. If they fill up their homeworld with research centers, they will never be able to build a space yard, thus never any ships or bases.
Further, if the AI does not start with a space port, it might never build one if it fills the homeworld with research centers. You might want to make them research the technology needed for spaceports first, before Applied Research. A planet filled with research centers is useless if they have no space port.
With no homeworld mineral miners, it might be a good idea to change the base empire resource production levels in Settings.txt. These settings determine how many resources an empire produces if it has no production of a particular resource, whether from facilities or components:
Minimum Empire Minerals Generation := 200
Minimum Empire Organics Generation := 200
Minimum Empire Radioactives Generation := 200
If the empire generates 1 mineral on it's own (eg: from a facility), the minimum minerals generation value is not applied and the empire gains 1 mineral per turn instead of 200.
Setting the minimum generation values to 2000 instead of 200 will allow the AI to make enough resources to build SYs, space ports, and research centers, as well as a few colony ships, before it researches any resource technologies.