I don't normally put my $0.02 in on threads like this, but it seems like the OP is actually trying, so I'll give it a go.
I've been doing some research, and from what I've read, the '99-'00 Civic Si 5-speeds should bolt-on directly and have the most aggressive gear ratios minus the final drive, which is 4.266, or the same as the OEM LS transmissions. So, I'd swap the final drive from the '98-'01 JDM ITR's, which is a 4.750. You can buy those from ICB Motorsports, but they are fairly pricey. Then, after that, throw on a weighted shift nob for better shift feel and firmness and add an LSD.
The transmission swap won't give you any more power, but it'll feel like it will and it'll definitely help with speed.
For power, B18b1's don't benefit too much from anything other than bolt-ons. If you have an intake and a header on it already, I'd add a header (with a collecter outlet size to match your exhaust diameter), give it a good tune-up, and call it good. If you want more power but you want to stay naturally aspirated, I'd consider a B18C1 or B18C5 swap or a low-hp wet shot spray setup.