Hi,
Aren't Livecycle forms awesome and annoying at the same time hehe.
1. Changing a form to flowable always shifts everything to the left, thats just how it is. My workaround for this is to build the whole form into multiple tables. You can still reference them in your code, but you have control over where things are positioned. Use blank tables for spacing in the form. Use multiple tables because the columns will always be connected even if you merge them. If you have two items you want to have in a row, make a table with more columns than needed eg. 4 columns - first item, small space column, second item, space to end.
2. Does it just appear to flow off the bottom of the form and not create a new page?? This will be because you need to select Allow Page Breaks within Content on the Object > Value tab. Any item that is bigger than the available space will move continue on a new page.
3. Not sure i quite follow your explanation, but it sounds like you want to repeat the subform. By adding a button and adding new instances of a subform, you can have new reports in new blank fields.
If you do use repeating subforms, you can number the instances simply with a textField initialize event:
this.rawValue = yourSubFormName.instanceIndex + 1;
Why +1? Because the instance count starts at 0. By doing this, the first instance of the subform will be numbered 1.
I wont go into creating repeating subforms because that is a much larger topic