Have you tried it with very simple cards too? (like, a midi synth without any irq or dma stuff)
Maybe you caused a short somewhere while cutting the mainboard? Closely check the edges for copper traces sticking out.

One would expect a piece of mainboard to be designed around the right impedance and everything. If it IS an impedance/crosstalk related problem, hand soldering wires might just mess up the signals even more...

I did check the edges and I did remove any tracks on the back that had no destination after the cut.
The board has at least one more layer (chances are it is a 4-layer board) inside so who knows what might cause the trouble...
The test ISA slot I used was soldered in ~1minute, you can't get sloppier than that.. but it worked perfectly - tested with a VGA. Didn't try any "simple" cards tbh , I gave it a stress test with vga+sb1.5 to ensure it really works.

Here i found a backplane isa board you are looking for:

http://www.ebay.de/itm/ISA-Riser-1-zu-3-PX-88 … =item5b14e22360

^ bjt is kind enough to give me one of the boards he posted , so I think I'll be set soon
thanks for the link though!