Running mutliple led blinkers off of the same wires won't affect anythying, even a couple of them wired together will still pull less current than a stock filament bulb, this sounds more like either a faulty wiring job, an intermittent short to ground or faulty flasher unit. Of them I'd prolly guess the wiring. How did you work the 2-3 wire conversion and did you run the blinkers in parallel or sequentially, TIP: if you ran them in series thats a no no. Will split the voltage drop across the two blinkers, which are designed to run off of 12 volts, not 6, which then might or might not trigger the leds depending on how much voltage the stators putting out atm. Run them parallel if they aren't already, ie; both hots and both grounds tied together. Don't really have enough info to properly troubleshoot this.

 

Best bet would be some non-insulated crimp style butt splices and some decent heat shrink. Failing that, the twist method will work if your on a budget since this is a pretty low current application, just twist them together and then down so they form a little ball when your done and wrap them securely in good electrical tape, not that cheap pvc garbage. Also, try to stay away from splice taps if you can, they aren't reliable in the least.