UPDATE
I re tourqued the head bolts yesterday. I seemed to work...kinda. There was no oil coming from the gasket while the bike was running, but there is definitely oil there now. It is supposed to be in the 40's this weekend. I think I will take it for a nice ride and see what happens.

 

Two heads gaskets and now a base gasket.

Do you let your bike get nice and warm before riding it hard?

 

Clean it thoroughly with some Brakeclean before riding it.

Less chance of being fooled by old oil.

 

Faast Ed the first 2 head gaskets were a result of an ignition coil issue. One was completely blown and the other was just smoked. In the past, I had not let it warm up enough before riding. Since my "enlightenment" I now let it warm up completely before riding hard. I do ride it hard, but not that hard! I am sure that it is not "old oil". It is leaking less that before I re tourqed, but none the less, still leaking.

I am fearing the bottom of the cylinder is warped. I will take it for a ride and see if it worsens or what. If it persists, I will pull the cylinder and take it to a machine shop for inspection.

I will say that the head bolts seemed really tight. Is it possible that they might have been over tourqed and damaged the gasket?

 

The proper torque is meant to allow for expansion and bolt stretch. (Thus the importance of a good warm up). You want everything fully expanded before putting the high rpm's on those head gaskets.
Overtightening likely wouldn't hurt the gaskets but it might cause some other problems. Depends on what type of gaskets and mating surfaces. You can kill some gaskets by over tightening but I doubt that you can with base gaskets. (Speculating there).

You should be able to ride hard. I ride real hard sometimes. But not unless I've been already riding softly for a half hour or more (preferably more). Nice and completely warmed up.

You very well might have some warpage and it's a good plan that you have (to check for that). Can't blame the Indy for that either.

I use Comtic head gaskets. Dang near impossible to blow. 42 ft lb torque, step up in graduated steps.

 

One question: Are you using the correct head bolt tightening procedure as outlined in service manual? Here is the excerpt from my 2005 XL manual:

The procedure for tightening the head screws is critical
to proper distribution of pressure over gasket area. It
prevents gasket leaks, stud failure, and head and cylinder
distortion.
10. See Figure 3-67. For each cylinder head, start with bolt
numbered one, as shown. In increasing numerical
sequence (i.e. – 1, 2, 3, 4), tighten head bolts in the following
steps:
a. Tighten each bolt to 96-120 in-lbs (11-14 Nm).
b. Tighten each bolt to 13-15 ft-lbs (18-20 Nm).
c. Loosen all bolts.
11. After head bolts are loosened from initial torque, tighten
bolts in three stages. Tighten in increasing numerical
sequence (i.e. – 1, 2, 3, 4), as follows:
a. Tighten each bolt to 96-120 in-lbs (11-14 Nm).
b. Tighten each bolt to 13-15 ft-lbs (18-20 Nm).
c. See Figure 3-68. Mark cylinder head and head bolt
shoulder with a line as shown (View A).
d. Tighten each bolt an additional 85°-95° (View B).
12. Repeat above procedure for other cylinder head

 

BTW, you can find a copy of the 05XL manual here: http://www.sendspace.com/file/h952ae