The issues don't seem too problematic and looking at the code it's just wrapping qrencode. So it should be trivial to fix the three issues mentioned. I'd just halve the chunk size and post-process the generated QR codes manually in a image editing program to put multiple of them on the same piece of paper, including some textual information. Then laminate that.
I'll actually be doing this soon I think. Previously I used http://www.jabberwocky.com/software/paperkey/ which is quite good, but it's like two pieces of A4 filled with text which would be a huge pain to restore.
I was quite surprised how much text you can fit into a single QR code nowadays. 2778 bytes of lorem ipsum generates a massive code (1000x1000), but it can still be read passively with an iPhone's camera. For comparison, a Google CA cert is only 1363 bytes. You could theoretically dump your cert and private key onto their own (big) single page codes, then just scan them back in when you later need it. That just leaves the possibility of your printer holding onto something it shouldn't.
Alternatively, if this is a "oh, shit" backup solution, you could just print and laminate the key, and enter it by hand years later, if necessary.
(This is just me thinking off the top of my head, mid-coffee. Ideas may be less valuable than they appear.)