1. yes, it is called stroking your engine......smaller piston's, longer rods.......very popular
2. yes, there are intakes on the market right now, that are carb intakes, that have bungs welde on them for fuel injectors and it works very well....believe one is called spyder.
3. That is a personal quest...some guy's like carb's, some like fuel injection....i personally like fuel injection, just for the fact that your computer help's make adjustment for your air/fuel ratio's....
If you bore the cylinder out, you will lower the compression but the amount is negligible. Compression is effected by your type of heads, pistons, cylinder volume. A posted 10.5 to 1 compression in reality is just close to that. Not exactly 10.5 to 1.
As for Carb versus Fuel injection.
Fuel injection is more effecient, but carburation is more responsive to sudden changes. Its a personal choice as both have pros and cons.
Next the FE head with a carb question, that would depend on the type of FE head (Direct injection, Port Injection ect..) and engine. You can use a carb with a FE head but remember its all about flow characteristics.
There is old saying about Horespower.
There is no substitute for Cubic Inches.
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