125-200cc My 2002 CR125 project

I think I have a budget in mind as to getting the bike running. Now I just need to figure out which direction to go. The bike before being assembled by an unknowing tech was as follows.

Stock bore with milled head PC works pipe and PC T304 silencer. Jetted accordingly

I can run this configuration if I had the cylinder sent out and use the piston Walt gave me a good deal on...

Option 2: stock 125 setup pulled from 09-14'
Option 3: 144 setup from 09-14'

With option 1 I imagine I may not even need to jet the carb since bike was local.
With 2 or 3 I am certain some jetting will be necessary.
I'm just wondering what should run the best. Still have the stock Mikuni which will be the most limiting factor

For general off road riding I'd go 144, either with the original top end or the newer setup. With the Mik you're always going to do some jetting If you're stuck with it just rebuild it, with a new float, get the JD jet kit and study the jetting thread. Better yet, post in the classifieds here and watch ebay for a used Keihen. You can sell the Mik to recover a little of the cost.