I guess it depends on what power you are making, and as you say, if the stock injectors are close to max'ed out.
If you do gain, it may only be higher up in the rev range, and you could loose a little torque down low.
I would say at around 100-110hp, it's not worth it.
I have one on order now for a 103.
We had Paul Hallam port/smooth the stock TB which should help some.

Seeing as you mention the TB off a 2006, I am thinking it would be a not unreasonable move. You could maybe go a used TC 96 version, must be plenty of them around.
Fair to say, the finish inside a SE 50 TB is not exactly "flowy" looking, but rather angular. Definitely worth a quick grind to clean it up.
However, I have a SE 50 TB still in a box myself, but am not putting it on until I do a 103(also all sitting in boxes, patiently waiting). But..... I only have a stock motor. If I had head work, cams etc, like you, I would probably put it on, I think.
A TB that is too large is really not your friend though.

I thought larger bore.
I researched it all a while back, and I was thinking that was the case, but cannot really recall. They may also be 46mm.
I should just measure,(and could) as I have all three here somewhere.
And, of course, the later manifolds(mid 2006 on, I think) have the 25 degree injectors.
I know when I had a quick peek at the 50 I have, I was amazed by how unfinished the inside was.
I knew immediately I would have to strip it apart, and clean it up.

Hilly, if your intersted, once we fit the 50mm TB, I will probably have the ported stock TB for sale.
It's from a 2009 Fatbob, done about 8000kms.
Cheers

Hilly ,,,here is a link for you I dont know if you've seen it but he seems to know what he's on about - he waffles on a bit but he seems to know what he's talking about its worthwhile watching the other podcasts about big boar / crank runout /heads etc....

http://www.youtube.com/watch?v=hjnzIlq90kM&feature=related

 

 

The butterfly is still 46mm, he just smoothed and port matched to his modified heads.
Not worth increasing the butterfly size, easier to buy a 50mm SE.

I have no doubt of the following......

Stock TB size is designed to add low end, so could never be said to be oversized.
Stock injector flow rate is adequate, but that's about it. HD are not allowing for any mods, as they have the SE 50 for that.
I fitted an SE 50 to a 103, and it really does work well.
I would not be planning to use the stock flow rate injectors, and especially not if the are the 8 degree ones(same flow rate).

According to the HD blurb:

This big bore throttle body features
a 50mm throttle plate (a 4mm increase over the ’06 Original
Equipment throttle body) ........... (that answers that question)
Higher flow rate injectors provide 25% more
fuel to complement the increased airflow.......injec-
tors (with a flow rate of 4.9 grams/second)

So...... in conclusion........
All you need now is a stroker crank ,and you are good to go.
(No need to thank me).

Is it rude to ask how much the heads cost ?

Hilly, that's quite a good price. The heads Paul Hallam did were a little dearer if I remember correctly, but I did get them
machined for Comp' release's as well. The 50mm TB turned up, just need to fit it, and find a useable base map.

Sorry to resurrect an old post guys but Hily, I was wondering how this was going now.

Also wondering where you sourced the kit from.

I am lookng at doing similar engine wise on a 2006 Lowrider.

Ride Safe
Nigel