I had that problem with the stock intake & 1/2" spacer. Now I use a GT-40 intake and no spacer without problems. I found that you could gain a little clearance by sticking washers between the hood and the hinges that bolt to it. The problem is that the hood will be sligtly raised in the back by the windshield and won't sit flush. It didn't look that bad though. Another option would be to get a cowl hood.
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1989 lx notch
89,000 miles
bolt-ons,stock heads/cam
60'- 2.07, 8.90@78, 13.93@99
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