You can use MSD #8228 coil as an upgrade, and with just a little wiring changes you can use a 6-Series box without too much trouble. MSD #32233 or 32239 should work - they are listed for 93-98, and I don't recall any changes for 91-92 and 93 - they'd probably work for 87-90 as well; although I usually make my own.
When you select your cap and rotor, make sure it has brass terminals rather than aluminum, since brass is a better conductor. I usually use Borg-Warner since they are consistently easier to find with brass terminals, but visually check before you accept the thing - I think most of the OEMR caps are aluminum, and about half of the aftermarket ones as well.
I'd also use Autolite Platinum plugs with that stroker - the electrodes are less susceptible to high-voltage erosion, and the electrode tips on those plugs do a better job of keeping themselves clean. You can usually find them for about $2 per plug, and I change mine every two years (just in time for Smog.)
Bear in mind that most rotor ends tend to be coated with something, so give it a quick pass with some very find sandpaper or emery cloth to clean it up - you don't want to remove any material, just make sure you have bare metal at the end, and that there aren't any burrs left over from manufacturing (those terminals are also usually stamped.)
Last and most critical - make sure you are getting a full 12VDC voltage to your ignition control - more is better. You should get full battery voltage there, which is supposed to be in the range of 13.6-14.5VDC. Take some time to make sure your ignition supply wiring is sound, or any mods you do are worthless.
Could you email me info on the header and the AFM you're using? I didn't know K&N made headers now, and Apexi isn't one of the AFR people I'd turned up. You might also want to look into the Adjustable MAP sensor mod, which will give you a little fine-tune control over AFR - and maybe relocating the IAT to the airbox to measure actual intake air temperature rather than manifold air temperature - which is higher. The lower temperature reading will result in slight fuel enrichment, which may help with your higher compression (since you don't mentione anything about quench.)
It would help you with fuel selection to know the Dynamic Compression Ratio of that setup - I can help you with that if you email me (I'll explain the whats and whys and how I got that number for you, if you decide you want it...)
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