I think you have a great little project here ! I have been considering doing this myself, I have a little garden tractor I'd like to convert!
First of all I think the arduino has the ability to do the job, however it will have to be optimized fairly well and you will prolly need to take a few shortcuts ...
If you already have points on the engine you could use that as your 1/rev signal ... You will need to determine the offset however,
You need to determine the relationship of your cylinders and crank, if both cylinders are beside each other and move up and down at the same time you can just fire both cylinders together on every revolution,
If you want to run continuous injection you can prolly use the pwm outputs at a sufficient frequency, depending on the injectors you decide to use the pulse length might be a few ms,
Use a mass airflow sensor ... Such as a Hotwire sensor , this will correct for inlet temp pressure and density,
Throttle position sensor will help you fine tune the system,
Using the once per rev signal ( interupt ) you will be able to calculate timer interupts for the spark and if you choose for the injector pulse,
After that you could add an oxygen sensor in the exhaust to trim the fuel air ratio,
Remember a carb is a very crude fuel metering device... It should be relatively easy to replicate, having a fully tuned fuel injection loop will be a little trickier ... But I have no doubt you should be able to get it running!