Perhaps you could outline, step by step, your process as well as the software tools (+versions)
I use dry film UV exposure (mainly, although I use toner transfer for masking pads prior to soldermask application).
Export the Gerbers (or from Fritzing export to PDF works too and that's what I originally developed the script to handle), and use my script to create a single PDF which has the artworks on a single page, my pcb's are usually small enough that it fits 2 columns and 3 rows so I can get 6 artworks (top & bottom, silk, mask and copper) on one sheet.
The artworks have an added frame, an indicator on a common corner (so you can mark the PCB's edge in one corner and always know "that corner goes there on the artwork"), and spacing between artworks that precisely fit a ruler/T-square to make alignment easier when flipping a board to expose the other side on a flat-bed (eg scanner converted into UV table).
I open the PDF in okular, and print it to tracing paper.
A quick check of dimensions with a ruler, but I've never had a scaling problem, and verify that your parts fit the footprints of course.
Expose (UV leds), develop (sodium carbonate), etch (cupric chloride), inspect (magnifying glass, multimeter continuity beeper) and fix (knife) any shorts. Strip the resist (sodium carbonate hot and strong, or acetone).
Print the pads-only artwork only onto exercise book covering (polypropylene contact film, any stationary shop) stuck onto paper, use this to toner-transfer onto the pads, run under cold water until paper soaked and board handle-able, peel off the artwork (no soaking or scrubbing required with this book covering technique). Repeat to get double toner on the pads if it seems necessary.
Airbrush with slightly thinned Pebeo Vitrea 160 (exactly this product, other similar ones don't work) available from many art supply shops in a variety of colours, when cured it forms a good imitation of a soldermask - durable, non conductive, soldering iron heat resistant and reasonably non-stick to fluxed solder.
Leave (approx 2 hours) until dry to the touch (ignore the 24 hour drying time that on the V 160 label, that's for laying it on thick, an airbrush layer is very thin)
Bake for 40 minutes at 180 degrees C
Cool
Use Acetone to remove the toner.
Drill, insert pcb rivets and solder and confirm continuity, assemble components, debug, throw against wall, resume debugging, lose interest, regain interest, debug more, achieve enlightenment, bask in afterglow.
I don't have a good way to do silkscreen yet. I guess you could use white Vitrea 160 for the soldermask and toner transfer to get black silk on white mask might be easiest, as long as you don't mind a white solder mask.
(These were single sided hence the jumpers, also, some bodging).