Majsta, you need to look into some better sources. You can get connectors made overseas for next to nothing (by comparison to the U.S.). You pay for the tooling and pin fixture. That can be a few thousand dollars. After that, you run as many as you want. They will probably be a dollar or so, depending on the number of pins. So, for 1000 pcs, I would be very surprised if you reached a total amortized cost of $5.00 per connector.
PCB protoyping is also very inexpensive now days. Do a search on alibaba.com, globalsources.com, etc. for PCBA suppliers. PCBA means both PCB and assembly. You would probably use a 4 or 6 layer board for the FPGA accelerator, and those are pretty simple to make. For two layer boards, I don't even get electrical testing done. If a company can't build a two layer board without issues, you should choose a new source. It's not much of a stretch to get 4/6 layer boards done. When you get into the 8+ layer boards, you need to really start watching your reject ratio. The suppliers I use currently build 12+ layer boards as a common daily build.
Getting BOMs quoted correctly is key. When your BOM calls for a resistor, cap, LED, diode, regulator, etc. do not give an actual part number as a reference - instead, give a specification and then request the exact datasheet for the part that is quoted in your BOM. I have found if you give a reference like a Digikey, Mouser, Newark, etc. part number that the price for your part is suddenly much higher than it should be.
ANY part that you are worried about being a counterfit - such as a FTDI, Microchip, Atmel, ST, TI, etc. buy it directly from the manufacturer. There are a LOT of knock-offs. Save money on the glue logic, PCB, and assembly, and don't skimp on the CPU, FPGA, PLD, etc. You can't afford to risk a knocked off chip coming back to haunt you later.