Hi Retro Soulman,
Boomy bass is a bizarre symptom in this case. Usually a product of too small cab volume and/or too high tuning. However in my view the cab may be too large! one reason low bass may be furtive, but that doesn't explain why the boomy sound, shouldn't be there with a too large box, and you already tried downtuning without success. On that specific aspect then i'd suspect some room issue Mike previously mentioned.
On the other hand, assuming the above shows nothing wrong, i'd look at this from a different perspective.
First, there's a thread here indicating the 4509 cab is the LF portion of the 3632 Cinema system, and called 3639 (confirmed by Tech Manual pic). I estimate box volume about 9 cu.ft, tuning about 40hz.
Second, JBL used the M115-8A woofer in the 3639 and later the M115H-1 it seems in that same box (see pic). You're using the 2035. I don't see the M115H-1 parameters in JBL's table but for the other two they are with the relevant numbers for box sizing and tuning:
2035H: Fs 48hz, Qts 0.34, Vas 140.5 L; M115-8A: Fs 46hz, Qts 0.39, Vas 225 L. Notable difference for Qts and Vas, both affecting proper cab size. In view of driver you use vs what JBL uses in the box my impression is the cab may be somewhat too large for 2035 use hence "not much low end." ?
Third, many bass systems are engineered for 2 Pi loading, meaning placement directly on the floor or in a large wall. Here its on stands, away from the floor therefore you don't get the full boundary LF acoustic reinforcement (no deep bass). The higher the stand is the more LF loss. Have you experimented with 1-2 boundaries (floor/wall)?
RE "I was thinking to fill the cabs with more material if that helps." Depends on the actual problem(s) you have, as well as the material you have in mind. If damping material, it creates virtual volume you may not need specially if the box is too large for the driver. If books, bricks or pieces of wood to reduce actual box volume it might increase boominess...
As for trying the 2205b in such box i don't see your situation improving bass wise, it could be even worst, i know since i have a pair of 2205H, and its low Qts 0.21 is a deep bass killer... The 2035 should do better assuming all is right. Are the 2035 really in good shape or might have an issue?
Richard
EDIT: Nice system you have. Has i anticipated your enclosures are pretty much off the floor, about a foot high...