99 Si would be optimum, but you can certainly just do some minor modding to your stock EX one and it will be fine, then save the money. You can't use the GSR harness at all. Only thing you need from it will be the plug/wires for the secondary intake solenoid, if you are using the stock intake manifold.
Moving dizzy guts is tedious but all the stuff is compatible and it will work, I've done this several times to ensure matching OBD plugs with the harness. If you need help hit me up I'll walk you through it.
No, you can't swap the shaft/gear over it will jack up your timing. Just the little black boxes with the wires on them, and of course the harness/plug which are attached to the black things anyways. It's tedious but you can do it. I just figured it out on my own and experimented with it and it worked great. D-series, B-series, VTEC, non-VTEC...it's pretty much all interchangable.
You'll probably have to extend the injector wires, and pretty sure the VTEC solenoid wires also. You'll need to relocate the primary O2 plug to the back of the engine. I don't suggest cutting it though, strip off the covering and pull it through, then retape it up. That's most of it. You will also have to add the ecu wire and ground, and the plug for the secondary intake butterflies if you're using a stock GSR manifold. Oh yes, also if you are staying with an OBD2 ecu you need to swap to the 2-wire crank sensor plug. You currently have 3 wires, I would repin and reroute the extra wire for the butterfly hookup.
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