Illustrator wont let me allign my strokes to the inside the align stroke bok to the inside is greyed

Your explanation is lacking what you are trying to achieve in the end, so hard to advise. Maybe you should use a fill instead. Or you can stack in appearance like this if you want one object.

The type of brush stroke you use can make a difference. I haven't competely tested this yet, but I had the same problem when the stroke that was being used was a 5pt oval. When I switched to a basic brush the panel options were no longer grayed out.

You can change the stroke alignment for everything except text which is what I'm guessing is the type of object you have that you want to change the stroke for. The only way to get an inside stroke on text is to convert the text to outlines first.

If you wanted to just add a stroke that appears outside the text you can do it with these steps.

1) Open the Appearance pannel, select the top right menu button, and select add new stroke.

2) Click and drag the new Stroke layer so it's under the Characters layer.

3) Click on the strokes layer and then open the strokes panel to modify the stroke as desired.

Granted this isn't going to get you strokes on the inside of the text but it will at least keep the stroke from choking the text.