Replacing the Timing Belt?

Timing belt removal:
Disconnect battery ground cable. Remove exhaust side spark plugs.
Remove fan shroud bolts and fan shroud, and position aside. Loosen, but do not remove, water pump pulley bolts. Remove accessory drive serpentine belt.
Remove fan and clutch assembly retaining screws. Remove fan and clutch assembly. Remove fan shroud. Remove water pump pulley.
On models with A/C, discharge A/C system using approved refrigerant recovery/recycling equipment. Remove A/C compressor from mounting bracket. Remove A/C compressor mounting bracket with power steering pump attached, and position aside.
Remove timing belt outer cover retaining bolt. Release seven cover interlocking tabs. Remove timing belt cover.
Rotate crankshaft in normal direction of rotation so that No. 1 cylinder is at TDC of compression stroke. Align camshaft, crankshaft and oil pump timing marks. See Fig. 1 crankshaft key-way should be pointing straight up, and circle on crankshaft sprocket must align with notch in engine front cover.
Holding timing belt tension-er with camshaft belt tension adjuster (T74P-6254-A) or equivalent, loosen adjusting bolt and pivot bolt. Slowly release spring tension. Pry tension-er away from timing belt, and tighten bolt to hold tension-er in place. Remove timing belt.

Installation:
Ensure crankshaft is set at TDC and camshaft sprocket timing mark and oil pump sprocket timing mark are aligned with inner cover timing marks.
Install timing belt on crankshaft sprocket, oil pump sprocket and then the camshaft sprocket. Loosen timing belt tension-er bolt.
Allow tension-er to adjust itself against timing belt. Do not tighten belt tension-er. Slowly rotate crankshaft clockwise 2 complete turns clockwise (as viewed from front of engine) so No. 1 cylinder is at TDC of compression stroke.
Recheck timing alignment marks. If timing marks are not aligned, re-position timing belt. Repeat timing belt tensioning procedure.
Tighten timing belt tension-er adjusting and pivot bolts to specification. See TORQUE SPECIFICATIONS: Install crankshaft pulley. Tighten center bolt to specification.
Install timing belt cover. Install exhaust side spark plugs. Install A/C compressor mounting bracket to engine. Install A/C compressor to mounting bracket. To complete installation, reverse removal procedure. Recharge A/C system, if necessary.

Are you getting fuel and spark?

You have the timing slightly out still put a thin screwdriver into number one plug hole rotate crankshaft clockwise so that the piston is on the rocking point between up and down. it needs to be right at the top point at the end of the up stroke before it starts to go down again. here is a better picture of the timing marks. I hope this helps. let me know.

It does not matter which plug hole you use on number one cylinder as long as it is at TDC and all of your marks are lined up. Ow battery power could be causing the rough running install the belt. I would not expect it to cause real rough running if all your mark's are set up correctly (right on the marks) then your timing is correct. Check all your leads are correctly routed and seated on plugs. Plugs are tight. Also, check vacuum pipes. Does the vehicle sit and idle now? Let me know.

recheck timing marks
do a compression test and a cylinder leak test