You have some different issues and here is one way you can approach them.
1. Different primary keys
You can create a new primary key and keep the old keys in a separate table.
By doing this you can still find an item with an old ID, but without messing up the table in use.
LegacyOperationLookup
OperationID LegacyOperationID Source
1 00215 Database1
2 46 Database2
This depends on if you have the freedom to change the design.
2. Different columns
If you have to similar similar tables but one table has some extra columns, or if both tables have a column the other table is missing, you have at least two choices.
a. You can create a new table with the sum of all columns.
b. You can create an extra table containing the additional columns as legacy.
The trick here is to know if the extra columns are useful in the new organisation or not and also if the columns can be NULL or not.
If no one will use the additional columns it is better to keep them in a separate table.
If the additional columns cannot be NULL, you have to decide what to insert as empty values.
3. PHP Admin
See this link
Merge two MySQL databases[
^] or use the same phrase in Google.
4. UML Diagram
Regarding the UML diagram I will not do that for you, but just give you a pointer where you can start to learn it:
TutorialsPoint: UML - Standard Diagrams[
^]
I hope this gives you at least some help forward.