Ok see if this makes sense.
1. You have 2 openings going to the back chambers from the tank.(Grates if you will) The pump pumps the water from the chambers into the main tank.
2. The first chamber is really just part of the tank because there is nothing to regulate the water level since the 2 grates allow the water unrestricted flow between the Tank and Chamber 1 and gravity will keep that chamber equal to the tank, blocking a grate won't help because you will still have a second grate allowing the water to equalize.
3. You removed the plastic from Chamber 1 to Chamber 2 which is what originally regulated the water flowing to the second chamber. There is nothing to slow the flow between the chambers. When people mod the wall between the chambers they only widen the gap between the chambers, they don't remove the entire wall across the top.
I think the only way to correct this issue is to put back the plastic that you removed because no matter what size pump you use, the same amount of water will be flowing between the tank and chambers since the wall regulating the flow has been removed. There was only one way for the water to leave chamber 1 and that was over the wall (which is no longer there). If you block the grates too much the pump will pump water into the tank and eventually it will overflow the entire back wall. (This would also happen if you were using a stock biocube filter and it became clogged or too dirty)
You need to come up with some sort of way to regulate the flow between chamber 1 and chamber 2. Maybe modifying a Stock filter reducing how much water flows through it, yet allowing enough water through to avoid overflowing the back wall.
At least I think this is what you need. :shock: