Not only make sure the knock sensors are connected, but you may want to pull them and make sure they aren't coated w/ coolant goo. The old Dex is known to coat them making them not perform as well, or at all.
Then be sure to use some thread sealant on them and torque them to the proper spec when installing or once again they will not read knock correctly. IIRC the spec is 14ft/lbs. You will want to verify this.
I would get a new longblock and go from there instead of piecing one back together that has already eaten 2 pistons. There is something wrong. Get a longblock, swap over your intake and accessories and call it good. With having a job right now the last thing you want is a "project car". You need to put something together that will last and actually get you to and from your new job, not leave you stranded w/ a 5 cylinder over and over.
For the cost of new head bolts (since stockers are TTY and not reuseable), HG's, LIM gaskets and various others to keep doing this over and over, you could have already found one for that price. Check craigslist for a good 3800 motor. Series II, Series III doesn't matter.
