Have the bores checked with a dial bore gauge for wear and taper before deciding to re-use the stock pistons. How do the main and rod bearings look, how much clearance? Do the rings rotate freely in the piston, or are they all carbon up?
Are you re-using the stock rod bolts, or replacing them and having the rods resized?
Inspect crank journals and crank run out and straightness in case the crank needs re-ground and bearings to match.
What condition are the cylinder heads seats, valves and valve guides?

I guess if it was me, and had a good short block, then I would leave the short block alone and put smaller chamber heads on the engine.
If you used something like the 78cc Trick flow heads, that should put compression around 9.5:1, already have new everything new including springs for aftermarket cam. That would kill your budget because of the cost of the aftermarket rockers arms, and hardware, but give you room to make alot more power later when you can afford to build a stronger short block.