best way to clear all iptables rules

To answer your question succinctly, no: there would not be any “leftover” rules after flushing every table. In the interest of being thorough however, you may want to set the policy for the built-in INPUT and FORWARD chains to ACCEPT, as well:

iptables -P INPUT ACCEPT
iptables -P FORWARD ACCEPT
iptables -P OUTPUT ACCEPT
iptables -t nat -F
iptables -t mangle -F
iptables -F
iptables -X

Clear ip6tables rules:

ip6tables -P INPUT ACCEPT
ip6tables -P FORWARD ACCEPT
ip6tables -P OUTPUT ACCEPT
ip6tables -t nat -F
ip6tables -t mangle -F
ip6tables -F
ip6tables -X

…and that should do it. iptables -nvL should produce this (or very similar) output:

Chain INPUT (policy ACCEPT 0 packets, 0 bytes)
 pkts bytes target     prot opt in     out     source               destination

Chain FORWARD (policy ACCEPT 0 packets, 0 bytes)
 pkts bytes target     prot opt in     out     source               destination

Chain OUTPUT (policy ACCEPT 0 packets, 0 bytes)
 pkts bytes target     prot opt in     out     source               destination