newbie, system issues

Just finished installing a new system in my SUV.  I put in sound deadening, an Alpine PDX 1.600 sub amp and Alpine 4.100 4 channel amp.  I am using a Tsunami 2 Farad cap with a power and ground distribution top.  the cap and sub amp are together under pass. seat and the 4 channel amp is under drivers seat.  I am using my Honda pilot H/U with out to an MTX Re-Q5.  RCA out to amps is Street wire ZN7. Polk component in front, coax's in rear door.  Sub in stock location is a Kicker, and subs to use when car not full are two Boston G510" dvc in a closed box wired to be a 4ohm load.

I've gone thru Alpines and MTX'x recommendations on setting up system as far as gains and crossovers.  I feel like I don't get much bass response at all out of subs,  If I try to add bass with gain adjustments on the Re Q5, I do get more but not the gut punch I expected with this set up.  Thats with the car idling in drive way.  Once on the road, I get a low freq hum as I accelerat e and the rpms drop back thru 2000 rpm and 1000rpm.  this does not go away until I disconnect either the rcas or the speaker leads from amps even with head unit off.  Or until I turn the gains down from the 12 oclock to nine oclock position on the Re Q5.  Then it is about 95% gone, but the bass (sub) is almost too.  I've been told the ground could be bad, as I used a bolt hole in floor of vehicle.  Also, the  Re Q5 unit is up behind glove box and ground is wired from there to same spot as amps to create a "ground loop isolator"  Also, because the 4 channel amp is by itself under drivers seat the ground cable from there to the common ground point is about 3 feet in length.  I did drill a hole to try and new ground point to no avail.  any ideas would be appreciated. thanks