Get yourself a replacement dowel pin. they're there for a reason. Don't "half ass" a top end rebuild. Always use new gaskets too!
A few questions...
#1... Are you re-using the old piston and installing new rings?
Thats how I'm reading all this.
#2... Did you measure the bore and piston to determine wear?
This is very important!
#3... Did you do a compression check before you tore it down?
What was the compression?
#4... Why did you tear it down in the first place?