So I have found that in fact I have GST in 90% of my inventory, and I am thinking about exporting my total cost and recent cost fields, Multiplying my Recent cost by Qty On hand and replacing my Total(actual cost) field with this number to reflect the cost more accurately without GST.

Any suggestions or issues you can see with this and should I know anything before I do this??

Also My G/L Inventory amount is not the same as my item valuation report I print out in inventory (only inventory account set printed).Off by a mile, even if i take into account the 5% GST. How is this possible??

Sorry, but you can't import the total cost field back into inventory. You'll have to import an adjustment, or perhaps a physical inventory worksheet.

Do you allow inventory to go negative? That's the most common reason the numbers don't agree. Also, don't rely on a back dated inventory valuation report if you're trying to get your numbers into line. Just print it out as of today.