Is a 50/50 mix of Acetone and Water inert?
Acetone is notoriously aggressive towards the plastic, rubber, and other non-metal components of internal combustion engines (and associated parts like fuel pumps). If the concentration of acetone is strong enough to dissolve your jell (assuming that is some organic compound) it is very likely strong enough to attack components of the fuel pump.  

As a bit of anecdotal evidence regarding what I said above, note that of the dozen-odd oxygenated additives allowed by the US EPA for the oxygenated fuels program, neither acetone nor any other ketone is on the allowed list. Although this is in part due to the high volatility of acetone, it is also largely due to the fact that acetone would attack engine components as described above.  

In short, what you've described is a bad idea for the health of your fuel pumps, even at very low concentrations of acetone.