Script Solution to Update Prices and Stock for Multi-currency Magento Websites

General information for the website: We sell CLothing Online
Description of requirements/features: We have persistent problems using our existing scripts to update prices and stock values on our stores from the stock control csv files.
There are three websites one for UK prices in Pounds, Two for DE and FR prices in euros.
Stock is global as is a Location attribute (used to help the warehouse).
There is variation in products across the different websites but all products are represented at a minimum in the UK websites.
There is are two stock csv import files euro and pounds both contain values for all product SKus.

Samples are attached.

We have problems with our existing scripting that include errors at various times

Scripts failing ungracefully leading to
Missing product needing to be resaved manually through status "enable"
Manual reindexing of stock, price and product association

Some Products showing as out of stock during and after processing leading to
Missing product needing to be resaved manually through status "enable"
Manual reindexing of stock, price and product association

Performance Problems with the Script taking 8 hours to update 14K rows even if not all rows need importing

A Successful bid should demonstrate

An understanding of the multi website magento environment and some of the errors we have encountered
Programmatic strategies to manage change over time to improve performance
Successful Error capture without excessive logging
Data Cleaning for inputs and graceful exiting of problems without scripting fails
Intelligent Cache and Reindexing

We don't want to inject SQL directly into the database.
We have tried a lot of different variations to solve these problems so no timewasters please.
We have Git/BitBucket repo versioning
Extra notes: