The cones are getting warm because the gain is all the way up. You're using the gain as a way to get the volume/loudness you want instead of it'* intended use which is to match the input signal from the source to the amp. This is a good way to blow subs. I feel your pain with that amp though, I would highly suggest getting a better amp and setting the gain properly like Cracker suggested. My gf has that same amp and even though I know better, I too set the gain crazy high just to get the volume cause like you said, the bass just isn't there when it'* set lower. I used to have an AudioQue AQ1200 in my car and it absolutely spanked that Eclipse amp and I didn't even have the AQ wired to get max power (1ohm) I had it wired at 2ohms giving me approx. 840rms to 2 12'* in my trunk and it was still waaaaay louder than that POS ZA1200 wired at 2 ohms (max power) to 2 12'* in my girls Caravan.

As for your box, I've never heard of audio enhancers but it sounds like some generic prefab to me, especially with the 40Hz tuning. That'* not to say that prefab boxes can't sound good, but it all depends on the build quality, internal volume, port area, tuning frequency, etc. Do you know how much internal volume that box has? Just to give you an idea.....your subs are being underpowered so in general you'd want a box on the large end of what Alpine suggests, so about 2 cubes per sub. If your box is only 2.5 cubes total then that could be part of the problem. I'd suggest building your own box out of 3/4" MDF, 4 cubes and tuned to 32-36Hz IF YOU PLAN ON KEEPING THE AMP YOU HAVE. The AQ1200D amp would make those things bang like you can't even imagine! My boy has that same exact setup in his 300 and it'* ridiculous, I was very impressed when I first heard it. That amp would only set you back about $249 and is rock solid! I hated to get rid of mine but I upgraded to a Sundown SAZ-1500D

i have a question about the chart on page one my amp is rms of 676 @ 2 ohms its infinity refrence 611a but when i downloaded the test tone and did what the chart said my amp gain was halfway up and it read 40 volts and all the way up was like 53 .3 volts does this mean that my amp is more powerful than infinity says or whats the deal i dont mean to steal anybodys thread im sorry

No, it means you should turn it a little less than halfway to make sure it'* set where it should be