Accurately calculating cost basis for positions

Placing limit orders for more than a few BTC mostly results in a long list of fills, sometimes over many minute during which price of both the target coin and BTC may fluctuate considerably. Trade history for most ecahnges does not list the BTC/USD value at the time of the trade and keeping this pair open on another chart may not be of any help in real time as fills can happen very rapidly. Some exchanges do not even list a XXX/USD pair for the target coin making it really difficult to accurately figure out the cost basis of a position. Using another exchange for the BTC/USD is not helpful as the price can be very different.

Anyone have any tricks for this I might not have thought of?

(Cost basis is an important metric for several aspects of trading, accounting and taxation so please no responses along the lines of why do you need that :/ )