Whats the difference between the questions... Have you made an application to the Home Office to remain in the UK in the last 10 years? and the question.....Have you been issued any visa for the UK, UK Overseas Territories or Commonwealth Country in the last 10 years? Obviously i had to make an application to get the visas.
The first question is asking if you have ever applied to remain in the UK.
The second question is if you have made any application for a visa either to enter the UK or to remain in the UK.
So, you answer yes to both - the first one being for your FLR(M) and/or ILR applications, the second for your initial visa to enter, plus your leave to remain application(s)
asks for a Home Office reference number I cant find any of my old paperwork so I dont have any reference numbers.
I believe you will only have reference numbers for visas issued inside the UK (FLR and/or ILR) - which should be printed on the letters that accompanied your visas when you got them.
If you don't know the reference number(s), then just leave it blank.