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I've been spending all day trying to achieve everything in my question.

The only solution I've found being to encode the subs onto a green matte and then key out the green in premiere and change the screen position and size.

The tricky part is scale and screen placement issue, I've tried handbrake, subler and ffmpeg, but without success.

Any free software suggestions are welcome. Thanks.

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If you convert the .srt files to .ass, then you can have a lot more control over how the subtitles appear.

To convert use ffmpeg:

ffmpeg -i input.srt output.ass

This will give you an .ass subtitle file. You'll see in the header of that file that there will be details about font, size, placement colour and so on. Here's an example from Wikipedia:

[V4+ Styles] Format: Name, Fontname, Fontsize, PrimaryColour, SecondaryColour, OutlineColour, BackColour, Bold, Italic, Underline, StrikeOut, ScaleX, ScaleY, Spacing, Angle, BorderStyle, Outline, Shadow, Alignment, MarginL, MarginR, MarginV, Encoding

Style: Default, Arial,28,&H00B4FCFC,&H00B4FCFC,&H00000008,&H80000008,-1,0,0,0,100,100,0.00,0.00,1,1.00,2.00,2,30,30,30,0

The first line lists all the settings, and the second lists the values for each style.

You can edit the header by hand to get the size and placement you want, and then burn it in using ffmpeg again:

ffmpeg -i input.mov -vf ass="output.ass" output.mp4

You may want to add encoding settings etc, but that's basically it.

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