actually, using race, contacts, and resources as 2 karma per BP results in roughly 475 karma, on average.
personally, i recommend counting 1 karma as 1 BP instead and giving about 425 karma. as i recall, each point of logic and intuition works out to being worth approximately 7.5 free karma for knowledge/language skills, based on the archetypes (mind you, that was all figured out assuming they were accurately made, which i understand now is not the case).
the only archetype in the books that can't be made is the troll enforcer, iirc (or whichever one has 9 str and bod, if not that one).
alternatively, you could go with SeCKSY (do a search for it, you should find it no problem) which includes a few other houserules too, such as making attributes cost more iirc... or maybe skill groups cost less? or both?
of course, if you want your PCs to be equal to starting SR3 characters, you might want closer to 550 or so karma to pull that off, i would guess.
if you wish to remove the limits, then i recommend either:
1) increase karma by quite a bit
2) count skill only for dice pool
3) wherever attributes only are used, stick with that.
4) change hacking/decking so that the program rating limits max hits, like the force of a spell does.
5) make higher rating devices of all sorts. currently, the only thing i can think of with higher than a 6 is the satellite uplink, which grants signal 8, plus some theoretical military hacking software iirc.
6) make the attribute limits attainable without cyber/bioware or magic. the attribute limit for augmented could then be removed, i suppose. naturally, anything beyond the racial maximum will cost more karma than normal to improve.
you'll have to work out defaulting on your own, though

of course, i haven't playtested this yet, so you may want to test this out before using it.
or, alternatively, you could just allow players to purchase the extraordinary attribute and the skill thingy multiple times per skill/attribute. this still makes it unappealing to boost them beyond sanity (20 extra karma for skills, 40 extra for attributes), but still allows them to do it if they want. if you do this, you probably won't need to change much else... so this is definitely the *easier* way to go, IMO.
personally, i like the wound modifiers the way they are, but if you want i suppose it's easy to do.
anyways, hope that helps.