Switched from 3ft to 10ft connection wires. My setup doesnt run correctly now. Timing issues?

A better solution would be to get a Pololu Wixel and companion shield for your Mega, and then put the Mega near the object. You can then program the Mega wirelessly and completely avoid problems with long signal lines. See this post for how I used it on one of my wall-following robots. You'll need two Wixels and one Wixel shield. They aren't particularly cheap, but you won't regret getting them.

There are other options for wireless control and programming, using Bluetooth rather than a proprietary protocol, but they aren't as easy to implement as the Wixel method.

The pins of logic chips and processors are not line drivers and will not operate properly when used as such. Sometimes you may get lucky but that generally would be intermittent in operation. They make drivers to drive wires off board from the controller and other chips that are receivers on the other end. This needs to be done with each digital line. There are some specialty drivers such as I2C repeater chips, RS485 etc. Remember the wires are antennas and the system is operating at a high enough frequency to be a great radio transmitter. The main thing is to isolate the controller wires from the world.