It is also common in old 6100s for the metal shield in the cover to sag or fall out completely. It is held on by little melted bits of plastic which by now are all brittle.

If you are installing the video card and sonnet card into a proper right angle adapter metal thing, it should prevent the lid from coming in contact with the video card, so your focus should turn to the spaces between the cards and the right angle adapter metal.

Another possibility is that your battery is dead. It will still make the startup sound either way, but will not boot. If you turn the power on-off-on, it will work with a dead battery. You may have coincidentally done this when the lid was off but not when it was on.