So currently I am the owner of a beautiful 2004 Accord V6 6 Speed Coupe 
I've had it for about 6 months and love it! Well long story short I was being a dumbass one day and misshifted into second from some hard driving and from there basically new it was time for a new motor. I kept driving the accord even though it was giving me the misfire codes from all cylinders as well as the random misfire code. I could hear a tick from my top end too but never got around to looking further into it as much as I wanted to cause I just didn't have time at the time. I had finally found an unmolested J32A3 that I purchased and continued my research. As I kept driving the accord it finally came to the point where the engine started knocking from the bottom end and at the point it was time for me to stop driving it and start working on this project. So the following is what I plan on doing with the J32A3 motor before I swap it in.
Cleaned & Sleeved J32A3 Block Bored by 1mm(90mm total) W/ Piston oil Squirters
J37 OEM Crankshaft(from 07-09 MDX)
J37 OEM Bearings
J37 Rods(looking at Pauter)
J37 90mm Wiseco 11:1 CR Pistons
MLS 90mm Head Gasket
ARP Head Studs
J37A4 PnP Heads with full Supertech Valvetrain
J37A4 PnP IM, Runners & TB
Gates Racing Timing Belt & Water Pump Kit
Unorthodox Underdrive Pulley W/ Gates Belt
So basically my total displacement will be 3.7 Liters tuned with a TL-S MT ECU connected to FlashPro. Once the motor is finished I will be running it all motor for a while up until next fall where I plan on giving it some boost. I will also be running my stock tranny for now but in the works of purchasing a 6mt W/ LSD & Axles from a 06 TL with low miles. As I am still collecting parts I still do have questions that are unanswered and will appreciate all the help I can get.
Are the J37A4 Heads with the Dual VTEC directly bolted on with the J32A3 Bottom End?
With the J37A4 Heads & IM, Runners, TB will any extra wiring need to be done or will my J30A4 Harness work just fine with the J32A3 Bottom End and J37A4 Top End?
Is the 07 Tl-S MT ECU directly plug and play with the Hondata Harness?
Is there anything else that I am missing for the build that I might need?
Any Suggestions?

I've had it for about 6 months and love it! Well long story short I was being a dumbass one day and misshifted into second from some hard driving and from there basically new it was time for a new motor. I kept driving the accord even though it was giving me the misfire codes from all cylinders as well as the random misfire code. I could hear a tick from my top end too but never got around to looking further into it as much as I wanted to cause I just didn't have time at the time. I had finally found an unmolested J32A3 that I purchased and continued my research. As I kept driving the accord it finally came to the point where the engine started knocking from the bottom end and at the point it was time for me to stop driving it and start working on this project. So the following is what I plan on doing with the J32A3 motor before I swap it in.
Cleaned & Sleeved J32A3 Block Bored by 1mm(90mm total) W/ Piston oil Squirters
J37 OEM Crankshaft(from 07-09 MDX)
J37 OEM Bearings
J37 Rods(looking at Pauter)
J37 90mm Wiseco 11:1 CR Pistons
MLS 90mm Head Gasket
ARP Head Studs
J37A4 PnP Heads with full Supertech Valvetrain
J37A4 PnP IM, Runners & TB
Gates Racing Timing Belt & Water Pump Kit
Unorthodox Underdrive Pulley W/ Gates Belt
So basically my total displacement will be 3.7 Liters tuned with a TL-S MT ECU connected to FlashPro. Once the motor is finished I will be running it all motor for a while up until next fall where I plan on giving it some boost. I will also be running my stock tranny for now but in the works of purchasing a 6mt W/ LSD & Axles from a 06 TL with low miles. As I am still collecting parts I still do have questions that are unanswered and will appreciate all the help I can get.
Are the J37A4 Heads with the Dual VTEC directly bolted on with the J32A3 Bottom End?
With the J37A4 Heads & IM, Runners, TB will any extra wiring need to be done or will my J30A4 Harness work just fine with the J32A3 Bottom End and J37A4 Top End?
Is the 07 Tl-S MT ECU directly plug and play with the Hondata Harness?
Is there anything else that I am missing for the build that I might need?
Any Suggestions?