The fact it has 10W40 and not 10W30 will NOT cause this issue, as for making it noisier, no it will help to make it quieter.
If the gap on each tappet is too large it will as said not fully open the valve, but I suspect that they are too small in clearance, after grinding the valves the valves have moved that bit closer to the cam, so the clearance reduces, holding the valve slightly open if bad enough but throwing out the valve timing as the valves are opening earlier and closing earlier.
Did you slacken the cam bolts so the pulleys could rotate slightly if needed, how accurate is the pin length that you fabricated, I'd be tempted to stick a ready made pin in the engine when timing or use a dti gauge, just to make sure everything is correct.
Just double check you have got a big air leak by having left something off, maybe overlooked tightening a air pipe up etc.
10W40 oil will cause NO DAMAGE what so ever, they are specified with a 30 weight oil for less drag better mpg etc, my dads zetec that I fully rebuilt around 7-8 years ago has used 10W40 from day one.
Engine flush will cause no damage, it can wash out varnish and congealed oil in hydraulic tappets and cause them to go noisy, but most modern flushes are little more than oils, and VERY gentle, older flushes could break great big chunks of carbon off, blocking oilways etc, not so now a days though.
I use a engine flush in all my engines cossie included 200 miles prior to the oil changes, not the recommended 10 minutes idling, and have just taken apart my 200,973 miles old cossie engine for rebuild, that is still on STANDARD CRANK SIZE big ends and mains, original cams, little ends as well, the engine was thrashed all the time, helping to burn off the contaminants in the oil keeping it fresh, hence it lasting so well.
tabetha