Before I start laying out the options, an aftermarket transmission is essential when you choose to stay NA (naturally aspirated) or going FI (force induction) route.
The current aftermarket transmissions available:
1. Dr. EVil with LSD ($4000)
2. Less expensive unit (different company) is currently being produced/tested
Custom J30A1 (Accord V6) - turbo application:
Option 1: stock J30A1 block/heads/IM/TB
Option 2: stock J30A1 block/J32A2 heads/J32A2 upper/lower manifold/J32A2 TB.
If I start all over again building the custom block with forged JE (9.0:1) pistons and Crower rods along with custom iron sleeves and new crankshaft I would definitely choose turbo path.
For starters, the low compression and stronger than stock listed internals can withstand up to 20psi or so. The current Comptech supercharger with supplied blower (Eaton/Magnuson model MP62) pretty much maxing out at 10-10.5psi, so it's limited in generating more boost if desired. In order to utilize extra boost, the next upgrade can be MP90 model which CT doesn't sell and can be purchased directly from Eaton/Magnuson distributors. However to fit the unit is the big issue since it's wider than MP62 and it also required to modify inlet/outlet to function properly. With that however in mind, if properly done that unit can spin enough to generate up to 15-16psi. Thus, in my opinion MP90 is out of the question and money required to make it happened (~$2500) can be rather invested in custom turbo application to utilize extra boost.
BTW, choosing the stock AV6 block is less expensive option since all you have to do is to keep your block and order just custom sleeves/pistons/rods and new strong stock crankshaft. I've heard from my installer as well as others Acura/Honda mechanics that Honda produce amazing crankshaft so that's a keeper.
Now back to turbo. Single ball-bearing turbo by Garrett is the way to go with the GT35 model. It produces full boost starting from 2600rpm all the way to redline. All other options are up to the owner and/or the shop who will be doing it.
Now, the famous cylinder heads and manifold questions:
Again the less expensive way is to keep the stock heads, stock manifold (upper/lower) and bore the stock 60mm TB (throttle body) up to 4mm when adding turbo. The J32A2 cam swap going to help some but I wouldn't change VTEC x point just leaving as it is.
The other option which is great is to get J32A2 (CL-S/TL-S) heads, lower (injector base) /upper manifold (intake manifold) and J32A2 TB. The gains here are great in mid-range and top-end. Even if you do a J32A2 cam swap into J30A1 heads the gains will still be less since J32A2 have larger intake valves along with larger round shape intake runners/ports, thus the air flow going to be significantly more generating extra power. In addition, stock J32A2 66mm TB can be ported up to 70-71mm getting even more gains.
This option is also perfect for choosing either J32A2 (3.2L) or J35A* (3.5L) blocks
Porting in polishing
IMO, the J30A1 heads/ manifold is not worth it since with the money spent the gains will be minimal. That is also applies to J32A2 heads/manifold since I've seen on cl board people gain very little with money spent.
Gaskets
If using stock heads/manifold just get stock gasket kits. Both FRONT cyl. head gasket kit ($171.48) and REAR cyl. head gasket kit (includes IM too - $83.96) can be purchased at hondaautomotiveparts.com (these prices are based on 2002 AV6). Also, both of those kits include 2 head gaskets that you place on the block and bolt it up both cyl.heads. In addition, I recommend getting new head studs (16) since they tend to stretch with added heat especially when you plan on adding supercharger or turbo (item called BOLT-WASHER (12X163) and priced at $5.38 at the same web site). APR makes great head studs, however not yet available for our cars.
When using J32A2 (CL-S/TL-S) heads/manifold you obviosly need those.
Both FRONT J32A2 cyl. head gasket kit ($136.66) and REAR J32A2 cyl. head kit (included IM too - $119.77) can be purchased at acuraautomotiveparts.org (these prices are based on 2003 CL-S auto). Again, both kits include important head gaskets and just in case you need them as a separate item it's priced at $27.30 each (need 2). Also, keep in mind to get new head studs as explained in the above paragraph. The head studs needed are 16 (8 for each head) they called "BOLT-WASHER (12X163)" and the price is $5.91 each on the above mentioned acuraautomotiveparts.org site. Also you would need to purchase 6 new CL-S fuel injectors rated at 270cc vs 250cc on AV6 and CL-S/TL-S TB (throttle body).
Keep in mind your stock ECU controls everything.
Finally the torque from the line would be nothing spectular untill your turbo kicks in
.
Advantage:
Custom internals provide best boost potential for turbo (assuming safe Air/Fuel ratio).
Disadvantage:
a. J30A1 pistons have to be modified (valve pockets metal removal) to have clearance for large J32A2 intake valves. This have to be done only if planning to add J32A2 cylinder heads, etc.
Updated valve specs:
J30A1 '98-02 AV6: 34mm/29mm (intake/exhaust)
J32A2 '01-03 TL-S/CL-S: 36mm/30mm
b. Torque is a little less than J32 but not significant as J35.
Summary: If plan to add turbo on stock J30A1 block - custom low CR pistons/rods are a must. If sleeves are in bad condition they have to be replaced.
The rest is simply bolt on. Higly recommend new engine/transmission mounts, gasket kits, new Denso Iridium IK22 plugs, belts.
If planning to swap stock cyl. heads with J32A2, J30A1 pistons have to be modified as mentioned above. You would also need the following J32A2 parts: injector base (lower manifold) including fuel rails, fuel injectors, upper manifold and throttle body, and new head studs.
Final word,
IMO, either keep stock cyl. heads/manifold/tb or get J32A2 short block along with J32A2 upper/lower manifold and throttle body. This would be a better choice since no J30A1 pistons or any modifications needed, therefore it will be a simple swap. However, keep in mind this option is better for supercharger since as mentioned Comptech blower is maxing out the efficiency and would be limited to run at 8.5-9psi with this option and 10-11psi with stock heads. These maximum values of boost are used assuming custom intercooler added with fuel management unit like E-Manage.
Also coming soon :
J32A2/J32A2 swap details (auto) -
for detailed 6MT list look somewhere else
J35A4/J32A2 swap concrete details (auto)
Xteam · updated 
MrV6P · updated 
