Creating Replication from scratch and do not want to change indexes or Procedures on Subscriber Servers

i have a situation here

I have replication from Server A (2008R2) Pub to B(2012) Sub for few databases..

I have 10 non-Clust-Indexes on X table on DB1 on A Server and non-Clust-Indexes 100 X table on DB1 on B Server

Now i have Upgraded server A from 2008r2 to 2014. side by Side, also implementing Always on AG)

I have to Create Replication from scratch A-B Servers

When i do from scratch, replication will wipe out Tables, Indexes , Procedures on Subscriber B, I have added many NON Clust indexes and Sp's on Subscribers Server B and i don not want to wipe those away...

How can i keep Indexes, SP's with out changing anything on Subscriber servers ?

is there a way to keep Indexes and SP's as it is? and just replicate only Tables and Clustered Indexes? and DATA?

Please guide on how should i proceed...