I think it takes 48 hours for merchant's money to respawn. Or you can use the trick i stated before: Save the game, kill the shopkeeper and witnesses and load the save.
Also, if you have high speech and the investment perk (can't remember what it's called), Riverwood trader can have over 10000 gold at once when you invest 500. Thieves guild merchant(s) also have like 4000 when you have finished the quests, i believe.
Speaking of thieves guild, did anyone else have trouble getting jobs for Markath? I've completed the special job for every other hold, but i just can't get Markath to show up..glitched, maybe?