I don't think you should have too much problem with the PCB and case / enclouser you have changed them so dramatically from the original design.
However I would redraw out the schematic, good measure change some of the part designation like R1 make R6, for added measure you can change some of the non critical parts, filter caps, led limit resistors, change led color, etc etc. As long as your not just going to a copy machine and copying it 1 for 1 you should be fine. If your using a micro you can change some code lines non critical so that when you view the HEX, it differs from the original, add a pointless loop, blink and led, or add additional functions recompile under a different software, etc etc.
And If your really paranoid, scrape off the chip numbers, use potting epoxy (that ticks me off, lol), use security fuses on your micro's.