New to yota and 4 runners. Advice suggestions on mods?

Hello fellow Road Warriors! I'm new to Toyota as well as for runners except for the eighties model old Toyota pickup trucks when I was a teenager. Man I didn't know I had the Holy Grail of a vehicle was back then. Before I digress to teenage mud stories. Bought a 99 4runner sr5 last week. Fell in love. What amazing quality vehicles in my God those little 3.4s! The first few days I had it I noticed it had a intermittent misfire. At 187000 I expected no less change the plugs learn my lesson about the Dual tip dual grounded plugs boom ran fine the whole day next day. misfire is back the day after, also get a random flashing check engine light had him run the code its number one cylinder misfire. the other two coils look like they had been replaced so I replaced it last night crunk just to make sure it would start what should I do next? Should I worry with a computer reset and drive cycles before I start just running it. When I get this worked out then comes the mods please any ideas for the two-wheel drive model since I can't really take it in the mud I was thinking about just more power. And looks. Thanks in advance guys and man I love these little things.
O I've also changed the plug wires and got last 6 denso dual electrodes and ran the seafoam induction through the bottom boot on passenger side. Not the brake booster.
Also slight rub/squeak from front passenger wheel area? Haven't pulled wheel off yet.