^^^^ This ^^^^ if they tapped into the wrong spot and you have bose no matter how good of a tune you give it then there will be missing range, because the sub plays a different range then the factory bose speaker would have and the bose is so integrated in with this car its kind of crazy. also check your Jensen amp, where they passed through your rca's make sure white is plugged into white and red into red I know this sounds trivial but it actually does matter for the polarity of the speaker.
on your Jensen amp it should have 6 turn knobs for adjustments and a few switches might be worth a look to see if they are set right, set the channels 1-4 in hpf to let the non bass get through and that's it, you want this slightly higher then your sub crossover.
it could also be you got a 3rd shift made sub setup and they reversed the polarity inside the box to the sub, take the sub out of the hole and make sure + runs to + on the speaker and - runs to - on the speaker, reversed polarity can definitely hinder the sound response, and bad. you must also remember 300w sub will not pound the block, it takes 1000w or more to really kick the bass. if you are used to the way setups of over 1000w sound try not to compare this to them, as it will never hit as hard.
this is out of your Jensen amp manual and maybe worth trying as well:
Crossover (X-OVER)
The Jensen Power series of amplifiers have built-in low-pass and high-pass
crossover filters for bi-amplifying the system. Adjust the crossover to
accommodate your chosen installation method. Select LPF (low pass filter)
when the amplifier will be driving woofers or subwoofers. Choose FULL when
crossover mode is not active and the amplifier is in “full range” mode. Select
HPF (high pass filter) when the amplifier will be driving full-range or separate
speakers, and you want to limit the “bass” being transferred to these speakers
Ill go a bit deeper in this too, the crossover you want around 140hz or so for door speakers (usually, I had alpine type s in my last set up and 140hz was perfect) set that and use hpf on the Jensen amp, then on your jl amp if it has one select lpf and set it just lower then what you set your Jensen to, then listen to some music you know well and listen for anything missing, is the mid bass weak, is the low end weak, is the high pitched too weak, then adjust accordingly and it maybe the Jensen has no crossover set and is on "full" (their setting for through) and it may not be passing the low signals correctly to your JL amp, try setting both 1-2 and 3-4 to high pass on the Jensen and see if that gets you more response from the sub, as the Jensen may not be passing the correct signals to the jl if set to full, as it would be trying to produce all of the range, if you tell it I only want high notes by selecting hpf and setting the crossover to around 140ish hz to start and then check again,that may solve your issues as well, because this may tell the Jensen amp to pass the low frequencies onto the output line and send them to the sub, each amp is different and I have no real world installation experience with Jensen, jl, jbl, Rockford, planet audio and alpine are the main ones I have experience with.
jl lists no spec for their box's port tuning frequency
Studum, where would you recommend he tap into for signal to his amp? he has a 4 channel for the door speakers that has a pass through rca for the sub amp, he has the sub amp on the 4 channel rca pass through for signal, I think you are correct if he has bose, the original installers may have tapped the wrong channels to get signal to the Jensen, so the Jensen may not actually be seeing bass signal to pass to the jl amp, I have bose but have yet to play with changing anything in it, as I just don't want to spend $200 to change my radio and find special speakers and what not, the stock bose sounds good for the prices to get more out of it or around it. I would suggest he follow the signal wires on the Jensen back and find where/how they got it signal and see if it is the front channels, if so would changing to the rear channels help, or would he need to tap into the sub or get an LOC and just make it go from line level to RCA, if this has not already been done