Two very important points about acrylic:
Firstly you need to use extruded acrylic sheet, not the more common cast acrylic. Cast acrylic won't vac form into anything but the most shallow shapes or gentle curves. Cast acrylic never goes beyond the consistency of a stiff sheet of rubber even at forming temperatures. If you're buying sheet, tell the stockist it's for vac forming.
Secondly the bubble problem is because acrylic is hygroscopic. That means it absorbs moisture. Freshly manufactured acrylic with the protective polythene sheet in place should be relatively trouble free but old acrylic is like to bubble horrendously at forming temperatures. This is caused by the moisture boiling in the plastic and it's not something that can be polished out. Commercial vac forming companies will always force dry acrylic sheets first by putting them in an oven for several hours before trying to form them. I know this because I used to design acrylic shop signs for one of the largest sign manufacturers in the UK and I still vac form acrylic to this day.
For a really good finish vac form a sheet of acrylic over your master, leave it on and then vacform a second sheet over this having first put cooking oil on the first sheet.