I installed a no name short shifter from ebay on my 98 EX and I still have the stock exhaust. and when I put it all back together it did hit in 3rd gear. I then removed a 1/2 inch thick piece of padding so it would sit a little higher and no more scraping, but it still makes funny squicking noises sometimes but I bought a nuespeed shifter bushings kit and Im think the padding isnt as thick as the stock, but I havent got it on yet.

I know this isnt on an Apexi, but maybe it will give you an idea if you know if the Apexi sits higher or lower than stock.