You would get a 9.77: 1 CR with the E88, and a 9.78:1 with the N42. Because the E88 has already had bigger valves put in I would use it, as I personally think it's a better head. The condition of both heads would be a consideration though. If you want a little more compression, you could use the 1mm HKS metal head gastket (these are excellent, but pricey at about $100.) You would end up with 9.97:1 with the E88 and the N42 would give you a 9.98:1 if you went with the HKS gasket.
It would help to use it though because of the higher compression, although the regular (fel-pro) gasket may do the job just as well. BTW, a freind of mine had the E88, L28 flattop setup in his car, and it ran, really good, and smoked my stock 83 turbo (it wasn't stock long after that!) He has since went through the bottom end, and put a knife-edged 240 crank and 240 rods under those flattops, but hasn't quite got it broke in yet. It should be good competition for those 3.1 strokers real soon. If anyone wants details on that settup just post, and I'll give them out then, as I've rambled on forever, on this post.
Z ya ll8er,