Inverted Fluid Balanced: Automatic Transmission vs Engine Oil

EDIT:  1996 3.8L Supercharged, 4T60 Transmission

I recently replaced my vacuum modulator on the transmission as I was seeing white smoke and there was transmission fluid in the vac line.  I just added a few quarts since when I last checked it it was low.

I've added 2 quarts and it's still well under the "Add 1Pt or .5 Quart" level.  I checked the engine oil out of curiosity and it was WAY past the max fill position.  I didn't smell any ATF in it and it didn't look red, but I have been noticing lately the "Check Oil Level" light has been staying on what appears to be longer over the past month.  I am concerned that ATF has been bleeding into the engine oil.  What would be the cause of that?  The front pump seal?

I've also noticed that it's hard to start, it stops like there is a little fluid in one of the cylinders, then kicks over and turns on.  I have a hydrogen fuel cell on it so I was thinking that it might be a slow steady build up of water, but with it being left off and the smoke persisting along with the vacuum modulator having ATF... I am being to led the transmission was the real culprit.  

I was thinking the hydrogen cell was doing carbon cleaning so I drove.  It didn't seem to have any problems until the last time I drove it before I identified the modulator.  The transmission seemed to hesitate to shift, so that led me to check the lines for the modulator and then the transmission fluid afterwards when I found it was low and stopped driving it.  

Is it possible that my transmission fluid is emptying into the engine?  How could I deduce that?  

I also noted on the inside of the coolant cap what appeared to be slightly gummy black deposits similar to PCV deposits....  I sense at the minimum that the lower intake manifold gasketing should be replaced.  I'm going to stop driving it until I get that squared away.

Any and all wisdom is much appreciated so thanks in advance.  I just bought this this year to be a reliable driver but the more I take things apart here and there the more I realize this old guy I bought it from did either his own shoddy work or used the services of a shade tree mechanic, which doesn't instill confidence.  He mentioned the supercharger bearing for the pulley was replaced so now I am wondering how long that'll last before I find out just how bad that went.

I also found what looked like old burned engine/transmission fluid directly on top of the transmission as if it had leaked down and spread out.  After I shut off the engine before its fully warmed up (just after I added the 1st and 2nd quarts) I hear what sounds like water burning on the exhaust or something to that effect.  Does it for 15~ seconds then goes away.  It also sounds like it could be electrical, but I am unsure.  I saw faint white smoke that I couldn't determine where it was coming from.

The top of the transmission with the fluid that seems to be automatic:




2nd Photo:



Underneath the superchager there appears to be engine oil that is pooled up in the crevices on top of the head (impossible to get a good picture with my camera), and then there is also this black cap which isn't for the AC or anything else I saw under the hood.  I'm not sure what it's for but if I want to get it out it looks like I'll have to remove the supercharger:

Disregard this post. I checked the engine oil while it was running. The Transmission might have been on the low side slowly being drained by the modulator for quite some time, and I'm pretty sure I need a new battery (hard starting problem is too consistent, and I recently gave it a few days of recharging to solve the problem it gives me now with the hard starting) I don't know why I forgot about that. !

Just some thoughts:

Consider replacing the supercharger plenum and lower intake manifold gaskets.  Time consuming but not difficult at all, be sure to get new bolts.

Your picture is too close for me to tell, but I think the black cap you refer to is just the Schraeder valve on the fuel rail for the injectors. It's where you connect a gauge to read fuel pressure on the rail.

You replaced the vac modulator with what?!?  Might want to check it again to be sure the vac side is staying dry.

Define 'hard starting' for us -- Rivs in good condition start *fast* but there's different things to look at depending on how the start is going.  Might be a sensor flaky, might be  a fuel rail pressure regulator issue, might be - might be... anyway let us know. Battery could be the issue *but* my Riv will start just fine, above freezing, with a battery that has essentially no cold cranking output.

What does the ATF look like? It might be time for a dump/fill or flush (depending on prior maintenance) change anyway.

Won't start and won't crank are not the same thing. I see threads all the time that don't make that distinction, and I always ask.

CoffeeCommando wrote:

The top of the transmission with the fluid that seems to be automatic:

What coolant do you use, is it green or red? If red, I'm pretty sure that stuff on the top of the transmission is dried up coolant, which dripping from the throttle body gasket. If you intend to replace intake gaskets (and you should), just make sure you get gasket set with all the miscellaneous seals and gaskets, throttle body gasket will be included.