Was the inner to outer cowl originally spot welded to the inner cowl?
Yes it was spot welded
...pic... ...pic... ...pic... What is the proper way to attached the inner cowl to the floor pan?
...pic... It welds to the floor pan/rocker.
There should be a flange at the bottom of the inner panel
...pic... ...pic... Here is the kick panel after reworking it to fit
...pic... The factory assembly manual has very good detail on this