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If you can, balance the moving parts, companies that sell race performance parts often sell tools for balancing as well, having your pistons and crank shafts all weight the same is going to make everything turn more smoothly.
from what I've read about intakes, a rough intake tends to help with the fuel/air mixing so that you get a more complete burn, so polishing the intake can be a bad idea, also take a look at tuning web sites that have exhaust calculators for sizing your exhaust system, larger is not better, you want your exhaust tuned for the engine size and RPM that you want it to perform best at.
If you can, it might be worth finding someone who does cryogenic treatments, when you properly cool metal down to -300F the structure changes on a microscopic level, I have to blades for a block plane for wood working that are of the same alloy of steel, one is cryo treated and the other is not, the differences in how they wear is amazing.
To me it seems like if you need to replace the engine that it would be well worth buying a new/used engine and rebuilding that, you would then keep the use of the car while doing the rebuild and would be starting out with an engine that might be in better shape, you might even check around and see what a brand new block would cost, for some vehicles they are amazingly cheap.
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