Hi Peter,
Any work on a previously machined part can be a bit daunting but pinning is not particularly difficult either to do or disguise though the latter is not quite so easy on the ball ends.
When you say ‘hand drill’ I’m assuming you mean on a drill press. As long as you can hold the work piece rigid under the drill on the drill table you should have no problem.
Ideally pins should be mild steel – I have used silver steel in the past and as this is more likely to be available in smaller diameters it’s okay to use but anything hard like piano wire is not.
Centreing can be a problem as if the pin is small then the centre needs to just be deep enough to allow the drill proper to be able pick up. A turned 120 degree point hardened out can be sufficient if gently pushed into the workpiece. Keep the drill well up in the chuck to gain maximum rigidity and drill through just deep enough into the shaft for the pin to work.
Don’t debur the hole – can’t stress that enough – cut the pin to length such that it will protrude about half its diameter, put a touch of Loctite on the ‘pin’ then tap it gently in the hole. Hold the part on to a soft support – eg ali and lightly tap the pin to swell its top area then clean any residue of loctite off – Meths is ideal for this. Once set the pin can be gently filed down to the surface using a fine needle file and emery. If you have deburred the hole you will have a ring to bear witness it’s been pinned but if you don’t in all probability you will find it hard to see

I think there are some pics in my album showing this op but you will have to go back quite a few pages to find them
Of course depending on it’s usage it may be that Loctite alone will be sufficient as it has remarkble strength if used correctly ie the right fit and the correct type – ‘601’ would be ideal.
Hope this helps – look forward to seeing the finished engine
Regards – Ramon