Big O – I would never consider a heat-transfer method to finish an enclosure. It is, as you’ve discovered, too problematic. Here are a couple of links to what the methods I have tried and prove to be quite effective. Easiest is Barry’s “Photopaper, stick-glue and ArmorAll method: Photopaper Method.
The method I use most often is the waterslide decal method. Here is the link that for me started on waterslide decals: Waterslide Decal Method.
Another method I have the print stock for, but have yet to try, is vinyl sticky-back print stock. You can get it in clear background or white background. It is probably the easiest method, but also quite unforgiving if it not placed exactly correct the first time. I’ve no links for this process, but Google\YouTube can help you out if you are so inclined.
Another method is a lot more involved and first calls for a waterslide, photopaper or other enclosure waiting method. The Epoxy Method.
There are also “etching processes that I have never explored, other than to admire the work of those who got the process down to a scientific art. I have no lies for that, but Google will fill your dreams.
I know none of addresses your process issue(s), but hope some of this helps.