I see that you already decided not to do the Si with VX tranny swap. If you are still thinking about getting the Si, know this: The SI does not have bigger front brakes! VX rims fit with no issues. The only problem is when someone does an Integra brake swap. If the brakes are stock then you'll have no problem. I know this because I have a '93 Si with VX rims. If the brakes have been swapped you can run HX rims but there is some slight modification (read: grinding) that needs to be done or use wheel spacers. Search HondaTech for a write up.
Also, the Si wiring harness has no provision for EGR, in addition to the 5-wire O2 sensor problem mentioned earlier. Even if you get a VX engine with its harness, the body harness that connects the engine harness to the ecu is missing the extra VX only 6-pin connector that carries the additional O2 information as well as EGR info to the ecu. Then you also need to get the EGR control box (black box that mounts to the firewall with vacuum tubes going in and out) and wire that in as well. Honda for some reason sends the 2 wires that control this thing not through the engine harness but through the wiper harness that goes through the firewall on the driverside. Annoying.
Si's also have power steering. Milers don't dig on power steering. You can bypass it but it will be really stiff. Honda-Tech has some threads on that, too.