Do not despair.
Your speakers will be quite capable of good sound at reasonable volume though they're not going to compete with huge disco earth moving equipment.
Read this article on IPOD earphone output:http://members.chello.nl/~m.heijligers/ipod/Performance/measurements.html
those folks preferred the IPOD's line output to its earphone jack. Note their remarks on distortion.
For a sanity check I went to a different speaker design site. You ought to try it out, here's the link. http://www.mhsoft.nl/spk_calc.asp#sealed
and a writeup on enclosure design.http://diyaudiocorner.tripod.com/dilemma.htm
It lets you plot frequency response. Type in the numbers for your speaker. First time it tells you to build a HUGE enclosure, like hundreds of liters.
That's for theoretically perfect damping of 0.707 . So type in Qtc of 1.3 and it gives the number we used for target volume.
I experimented with Qtc's until it produced your as-built volume of about 35 liters then hit 'show frequency response'. Qtc around 1.2 is what we appear to have. Volume appears not overly sensitive to Q, meaning we're not teetering on the cusp of some design criterion..
Plugging in the numbers from your speaker and tweaking Q to make program produce your as-built volume I get a Q of about 1.2125 This gives a slight (3db) peak in response at around 70 to 150 hz. That's going to sound pretty "bass-ey_". True hifi purists would call it 'boomy'. That's why i suggested it for your first project, it's what we like in our youth - i know I did and it's how i still listen to old r&r!
Now a Q greater than 0.71 means the enclosure has a resonant frequency around which the cone travel will be more than you'd expect. We have used this phenomenon to exaggerate the bass response of your speakers in anticipation of a low powered amplifier. A high powered one might overdrive them in the 70 hz range. That could be what's going on if Dad's amp is high powered , and judging by your description of his speakers I'd guess he has really good stuff..
When troubleshooting one always tries to split the system in half isolating the trouble.
Our first split is: source (amplifier, ipod) or speakers?
So first thing i'd try is swapping to line output of that Ipod. Might take a different plug.
Watch cones - can you see them moving much?
If it's resonance the problem should go away with a smaller amplifier.
Strictly speaking the amplifier output characteristics should go into the enclosure design but that's a refinement that is seldom aplied. It is conceivable (but unlikely) that dad's amplifier does not expect underdamped speaker system. If you can find some telephone wire, that small #22 solid stuff, put a few yards in series with the speakers. That'll make them look more resistive which increases damping and decreases Q. From the speaker's point of view it makes the amplifier's output impedance look a bit higher.
If it is resonance and it doesn't go away there's other things to try. I was going to suggest venting it but the calculator programs are giving far out results. Might be worth an experiment though anyway. Do you have enough material to make another top for experimenting? If so make one with a hole in it to fit an inch & a half sink tailpiece (plastic, about $2 at hardware store) and see what that does.
Sooo -to summarize
try LINE out on ipod;
if amp has a button labelled "10 hz" or "low filter" try it;
try it on a FM radio station which won't have sub audible bass in the signal;
try some telephone wire in series;
that should answer "source or speakers ?"
gently push the speaker cone in and out with your fingers listening for sound of something dragging;
try a full gallon jug inside the enclosure;
try a sink tailpiece a foot long in a temporary experimental top.
one must experiment to learn anything.
keep up the good work!