no need to update registry, put it in startup paramaters via enterprise manager along (right click server, properties) with the -e, id, -i. Just add another entry -n

if you start...

you could start sqlserver with the -n flag, then sql server events (ANYof them) are not posted to the windows application log

I have never heard of microsoft not recommending this option. You just need to be sure each individual node is capable of supporting both instances should it become necessary. (particularily...

statistics and indexes available are the main determinants for execution plans. Check stats are up to date, try updating them then checking execution plan.

degre of parallelism is another potential cause....