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Depending on how much motorway driving vs fast road etc you might want to switch to a different gearbox i.e motorway driving you might want a D16 box, or fast roads and town a D14, better get-up and go just a shorter top end ratio gear. Be aware that although most are identical the EP/EU shape models have a slightly different bolt position and some have a different spline count on the shafts - Go for (EF/CRX upto EJ/K) 88-00 and you'll be fine

Sounds serious bud. Might be worth taking it apart again like krzys says, although not a lot you can do with gearboxes if you're not a specialist. You'll find a d series gearbox in most breakers yards mate, very easy to come by. Phone some local breakers and ask if they have any 1.4, 1.5 or 1.6 civics in. Even one from a 3 door should fit I think.

That doesn't sound good at all, if you've had it apart once before is it not opening it up again to see what's happened? For an MB3 any D series box should do the job.