*random, intrusive advice*
I buy all my CDs & DVDs from the Japanese HMV because I am impatient. CDJapan is decent only if you select slower shipping methods because it drastically overcharges shipping, & in my experience (& friends of mine) is terrible when it comes to stinging you for customs/import taxes. Their items are generally always cheaper too. A while back I put all the versions of Holy Grail into my shopping cart & went to check out to compare prices. Here's the difference:
(note: these are multibuy prices. If bought alone the deluxe edition costs ¥3,221 & the limited edition is ¥2,833)
HMV
Deluxe edition: ¥3,108
Limited edition: ¥2,734
Regular edition: ¥3,000
Shipping: ¥1,800
TOTAL: ¥10,642
CDJapan
Deluxe edition: ¥3,790
Limited edition: ¥3,333
Regular edition: ¥3,000
Shipping: ¥5,340
TOTAL: ¥15,463
I'm not confused. HMV's limited edition really is cheaper than the regular one. The shipping method is EMS because this is all HMV offers. It's the quickest for overseas purchases. Usually takes 2-3 business days for me. It's trackable & insured. CDJapan's cheapest method, SAL, costs ¥1,700 (a whole ¥100 cheaper than the fastest method with HMV, lulz), isn't trackable or insured & takes 1 - 3 weeks.
I've never had to pay customs fees with HMV, but my Swedish friend has. I think that's probably because we have HMV stores here in the UK.
However, HMV doesn't accept Paypal. But it also doesn't charge you until they ship your order. Their shipping fees are liable to change because they only give you an estimate (usually for box sets & books, so the deluxe edition of Holy Grail with the photobook falls into this category). It happened to me with a stack of magazines, but they e-mailed me about the change first asking if I'd like to continue with the order & it was only a few hundred yen extra.