MySQL query optimization for legacy application
SUGGESTION #1

You have no meaningful indexes. That can have a detrimental effect on execution since the MySQL Query Optimizer has no help in searching.

You should all the following indexes

ALTER TABLE customers ADD INDEX bigindex (status,deadlead,purchased,last_updated);
ALTER TABLE notes ADD INDEX timestamp_id_index (timestamp,id);


This may help with some of the searching

SUGGESTION #2

You have duplicate indexes. That can slow down INSERTs and bloat the MYI file.

Please run 

ALTER TABLE customers DROP INDEX id,DROP INDEX id3;


SUGGESTION #3

Periodically, perhaps once a week, you should update index statistics

ANALYZE TABLE customers;
ANALYZE TABLE notes;


CAVEAT

There could be other things I could suggest. However, if the amount of data is relatively small, indexing is probably all you need.

Give it a Try !!!