The challenge will be automating the device so it 'knows' when the board is done... My first thought was some overly complicated system where it runs a short etching cycle, then rinses and checks with an IR camera or something to 'see' if the lines are distinct enough, if not continue, etc.... Another would be just a simpler system where it etches for a short cycle, rinses...then shines a laser across the surface and measures the distinction... if the trace edges are sharp enough, it knows its done...
Obviously, this is going to take some experimenting and playing around with... but I think overall, the outcome will be worth the effort.. I'd like to make it as low maintenance as possible...as little mess as possible, and as simple as can be.... liquids are tough to deal with to begin with, let alone acids and other toxic chemicals... so that'll be another challenge...
If anyone knows of any cheap small pumps capable of pumping the muriatic acid/hydrogen peroxide mix, I'd be happy to see... I've seen a lot of back and forth on SHURflo pumps...
Santoprene is a material used in pump components which has good resistance to acids and H2O2. A quick search indicates some of the Shurflo pumps have santoprene diaphragms.
http://www.oecfh.com/downloads/aro-chemical-resistance-guide.pdf
http://www.salhydro.fi/files/PDF/SantopreneChemicalResistance.pdf
Also, peristaltic pumps can sometimes be found cheaply (often as dishwasher spares) and can be fitted with santoprene tubing. The downside with these is the flow rate is usually very low but they do produce good pressure. It may be possible to use a them with some kind of nozzle for your application.