Hesitation in 2nd and backfire at 3500

I got my engine back together with the parts in my sig. I set the timing to 10, when I drive around the block the car works perfect in 1st. As soon as it shifts to 2nd there is an hesitation when I press on the gas. When I punch it the car accerlates but then there is about two or three backfires and then the car takes off. I tried adjusting the timing up to 12 with no luck I did not want to got higher since I am not familiar with check for pinging. I tried cleaning the MAF the only things I can think of are the engine is not getting enough fuel until I punch it but I can figure out why it works in first or the timing needs to be set higher. If anybody else is running what I am what degrees do you have the timing set at? Thanks for the help.
 
I changed the plugs with no luck. Just put on new cap and rotor and plug wires only have 3K miles on them. I checked the wires to make sure the firing order is correct and added injector cleaner (injectors were taken from a mark VIII with 70K miles on it and they looked fine)
 
I went to drive and checked the wires to MAF sensor and wires to injectors. I noticed the backfiring is gone but the hesitation is still there. I noticed that from 1K to 1500 is where the hesitation and rocking of the car is but after 1500 the car runs fine. Car was sitting for 4 weeks while I was getting parts for the engine thinking maybe sediment in fuel.
 
It is coming out the exhaust, the heads had autolite platnium in them when I bought them but changed the out with the +4 ones that I had to see if it was the plugs causing the problems but both plugs were doing the same. I pretty sure the timing was stock at 10, i didn't check, today i adjusted the TPS and it got a little better, then noticed a sensor next to the vacuum tree on the firewall had an open hole, i put my finger on the hole and the idle seemed to run better so I put a plug on it. I also adjusted the timing to where the engine sounds perfect with no loping and the inital timing was at 20, i think its to high but the engine sound goods. I took it around the block and on the highway and accerlation was fine, a little slow IMO with all the mods, but only backfired once in accerlation and car was fine except in the 1K to 1500 range in any gear.
 
MAP BAP

OK. Since you have afterfire instead of backfire, I'm guessing you're running rich. The sensor that you are talking about is most likely the MAP unless your 88 is a California car it which case its a BAP (or BP). Both these vary the air/fuel ration based either manifold pressure (MAP) or barometric pressure (BAP) and could easily be the cause of your problem. The MAP should have a hose running to the manifold, the BAP should be open to the atmosphere. Either way I don't think that capping the connection is the way to go. I suggest that you do a search on BAP MAP and go from there. Also, 20* seems like a lot of advance, my crate engine likes 18-20, but I'm running at 16 while I verify if the timing ring has slipped.

FYI if you have a MAP the sensor should have a standard hose connection for the vacuum line. If it's a BP the opening should have a white ring around it that looks like a cap with a hole in the center.
 
My car is a cali car and there is a cap but it is black. I noticed that when the spout connector is in the timing goes to 24. I had read that when you set the timing to 10 the computer is supposed to go to 24. I was wondering if that could be the problem, there computer is not setting the right spark advance. I did notice that the was a strong smell of fuel I will check the inlet tube to make sure C & L sent me the right one.
 
I was noticing, while driving, that my CEL went off and it has never done that in the 2 yrs I have had the car. I had the codes read and it was that both of the banks are running lean with the cats gone I was told that was probably causing the problem the light stayed off for six seconds and came back on. Also don't hear the backfiring any more.
 
Hesitation

Can't help with the effect of the cats being gone, I'd research this forum on that. If you have a BP sensor then the fitting should be open to the air. 24# inj should be ok. You may have done this already, but before you get to far into all the things that could be wrong I'd check the fuel pressure, check the vacuum, check the timing ring for signs of slippage. If everything is good then set the idle at ~900-950 rpm, reset the TPS, reset the computer. With your mods I would expect that the car gets kind of jerky under 1500 rpms, but it shouldn't backfire or afterfire. Drive it for a while and check the plugs for signs of rich or lean and correct timing, and run the engine codes. If you need help, some research in this forum should walk you through all these steps.

Two things would give me the most concern; 1. Making sure its not running lean 2. That the timing is too far advanced and that is covering up an AF problem. As you probably know too much timing and a lean condition can be very BAD.

Good luck.
 
The backfire was only under WOT and it has gone away and it is only jerky under 1500 rpm, it sounds like that is normal from what you said. i will check the fuel pressure to be sure along with timing marks. Thanks for the help.