Always worth tidying the cases up when they are apart. The stock port timing is actually very good, but it's a good idea to optimise/equalise the port windows, and open up that boost port, as you noticed.

The casting flashing is ugly, and good to remove. Don't waste time knife-edging anything or polishing; there's room for a little turbulence! And don't raise the compression. A huge no-no with the NSR.
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Andy.
NSR-WORLD.COM

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