As a rotary nut, here are my obversations:
04-05.5 had these issues:
poor ignitions
poor starters
bad engine seal tolerances (potentially)
weaker transmissions through 07
the facelift ones have the more robust starter, less likelyhood of bad engine due to poor seal tolerances (engines are hand built, thats some AMG E36 M3 right there :P) stronger transmissions (top loaded instead of split case) with better syncros and gearing.
most of these changes happened after the 2006 model year but the new facelift ones are a lot more reliable and have better components in those aspcts:
things to check be aware of:
Starters
ignition coils, modules, plugs
Engine compression (but they have an 8 year 100,000 mile warranty)
Transmission (IE gear grinding look out for)
cats clogging
clutch pedal failure
The benefit of the 04-06 ones are that they are dirt cheap, an incredible suspension, easy to work on, mazdaspeed contingency program is A+ excellent and they are the lightest out of the rx8s, especially without a sunroof.
And I'f your over 6' I would only be looking for a sunroofless model, which means you have to stick with the cloth interior, which is arguably better but you wont get heated seats but some odd combinations will come cloth, no sunroof with navi.
I've done my research you can lol
I just don't have a worthwhile job to replace my mazda2 for one yet due to fuel mileage.
you can find sub 60k mile rx8s for 7-10k manual cloth...
or a wrecked or dead engine for the 3k range.
Modding them for power is really expensive and almost frutless, weight reduction is very beneficial. You can spend 1500 dollars on intake, full exhaust, no cats and a tune and pick up maybe 11whp.